Here's a list of what characters refer to one another as. The use of honorifics in Japanese denotes how close a person is to one another, or how much respect someone holds for that person. Not using an honorific either means the person speaking isn't being polite to the one they're speaking to, or they're so close that they don't need to use them between one another; whichever one it is matters the relationship of the people involved and their personalities (though some games choose to forgo honorifics entirely or with the exception of certain super polite characters, due to the fact that they aren't set in Japan).
The ones used in the game are...
-san: Most commonly used, mainly to be polite.
-kun: Used for men and boys, much like -san but this one is gender specific.
-chan: Most commonly used for girls, though sometimes also for a child, close loved one or family member (male or female).
niisan/chan or either with "o" at the front: variations on Big Brother.
neesan/chan or either with "o" at the front: variations on Big Sister.
anata: Literally, it's a polite way of saying "you." However, it can also be said from a wife to her husband, acting as a Japanese equivalent of the word "dear." It's the latter that's used here.
There are a few more, mostly familial references, but since they are only used once or twice I will explain them when I get to them.
To Ark
Just Ark (Ivy, Jester, Vanrose, Doug)
Ark-san (Claude, Ileyda, Philis, Telmia, Yurald, Jean, Eberle)
Ark-kun (Shelley, Doug [post Falcken], Rick, Diana, Jean)
Ark-niichan (Halley)
Ark-oniichan (Emmy)
To Ivy
Just Ivy (Ark, Jester, Vanrose)
Ivy-san (Claude, Ileyda, Philis, Telmia, Yurald, Jean)
Ivy-chan (Shelley, Rick)
Ivy-neechan (Halley)
Ivy-oneechan (Emmy)
To Jester
Jester-san (Vanrose, Shelley, Telmia, Rick, Jean, Eberle)
Sempai or Jester-sempai (Ark & Ivy; Sempai is a term used to refer to an upperclassman or mentor figure)
To Halley
Just Halley (Ark, Ivy, Vanrose, Doug, Rick, Jean, Eberle)
Halley-chan (Philis)
Oniichan or Halley-oniichan (Emmy)
To Vanrose
Just Vanrose (Shelley, Doug, Rick, Diana)
Vanrose-san (Ark, Ivy, Jean, Eberle, Halley, Emmy)
To Emmy
Just Emmy (Ark, Ivy, Vanrose, Doug, Jean, Eberle, Halley)
Emmy-chan (Ivy, Philis)
To Doug
Just Doug (Ileyda [talking about him])
Anata (Ileyda [talking to him])
Doug-san (Ark, Ivy, Vanrose, Shelley, Philis, Telmia, Rick, Diana, Yurald, Jean, Eberle)
Doug-ojiichan (Halley, Emmy; Ojiisan/chan & its other variants mean grandfather)
To Eberle
Just Eberle (Jean)
Eberle-san (Ark, Ivy, Vanrose, Doug, Ileyda, Philis, Rick, Diana, Yurald)
Mama (Halley, Emmy)
To Shelley
Just Shelley (Vanrose, Rick, Diana)
Shelly-san (Ark, Ivy, Halley [talking about her], Emmy)
Shelly-neechan (Halley [talking to her])
To Yurald
Shinpu-sama (Ark, Ivy, Vanrose, Shelley, Doug, Rick, Eberle, Halley, Emmy; with the Kanji used in the game, the word Shinpu means Catholic Priest...interestingly enough the Kanji for "father" is a part of it)
To Philis
Just Philis (Vanrose, Doug, Telmia)
Philis-san (Ark, Ivy, Ileyda, Yurald, Eberle)
Philis-chan (Shelley)
Philis-neechan (Halley)
Philis-oneechan (Emmy)
To Rick
Just Rick (Vanrose, Shelley, Doug, Diana)
Rick-san (Ark, Ivy, Ileyda, Philis, Yurald, Jean, Eberle)
Rick-niichan (Halley)
Rick-oniichan (Emmy)
To Diana
Just Diana (Vanrose, Shelley, Rick)
Diana-san (Ark, Ileyda, Philis, Yurald, Eberle)
Diana-neechan (Halley)
Diana-oneechan (Emmy)
To Ileyda
Just Ileyda (Doug)
Ileyda-san (Ark, Shelley, Philis, Yurald, Eberle)
Ileyda-obaachan (Emmy; Obaasan/chan & its other variants mean grandmother)
To Jean
Anata (Eberle)
Jean-san (Ark, Ivy, Vanrose, Shelley, Doug, Ileyda, Telmia, Diana, Yurald)
Jean-sensei (Philis; though usually meaning teacher, Sensei is also used for other authority figures like doctors)
Papa (Halley, Emmy)
To Telmia
Telmia-san (Doug, Jean, Eberle)
Telmia-obasan (Emmy; Obasan/chan & its other variants mean aunt)
Okaasan (Philis; Okaasan/chan & its other variants mean mother)
To Claude
Shashou-san (Ark, Ivy, Vanrose, Shelley, Doug, Ileyda, Philis, Telmia, Rick, Jean, Eberle, Halley, Emmy; Shashou is how you say Train Conductor in Japanese)
Due to how squishy the kanji looks I might have missed some people's references to Yurald, though this is most likely everyone who spoke about him. Also, if a character isn't mentioned as using an honorific for another person it means they never directly address or talk about him or her in the game. And yes, some characters do seem to use two honorifics for the same person, mattering the time and place.
I looked at each characters' usage of honorifics, and figured out their patterns of speech. This has allowed me some educated guesses as to what they would use for the characters they never directly refer to in-dialog. If they ever do make a sequel, and I get the chance to play the Japanese version, I'll have to see if these check out. Though I am leaving Claude and Yurald out of my guesses since everyone who does mention them directly seems to be using -san for Claude and -sama for Yurald.
Ark
He seems to use names for children characters, -sempai to show respect for his mentor, while -san is for most everyone else since they don't know one another so well. Since he just calls Ivy by name, it can mean one of two things. One, despite all their arguing, he considers her a close friend. Two, it's because they don't show respect for each other. However, considering the way the story plays out, I think it's probably the first one, or it starts with the second and becomes the first.
From this analysis, he most likely uses -san for Telmia, the only person he doesn't directly refer to in-game.
Ivy
Ivy's usage of honorifics is very similar to Ark's: names for children, -sempai for her mentor, -san for everyone else. Like with Ark, the fact that she uses his name can either indicate their Trust for one another, or a lack of respect. Most likely the first, or the second one turning into the first, since they have that unspoken Trust in-game.
Due to this, she probably uses -san for the three people she doesn't refer to in-game: Diana, Ileyda and Telmia.
Halley
Halley usually uses familial honorifics for people older than he is, reflecting their age and relationship. His usage of -san for Vanrose and Shelley might indicate respect for their authority (as Vanrose is the pioneer's leader and Shelley is the person closest to him), however it could also be due to Vanrose's distant attitude (since he does use the -neechan suffix for Shelley when talking directly to her).
In-game, the only people he doesn't directly talk to are Telmia and Ileyda. Since he and Emmy are practically the same in their usage of honorifics, he probably calls them "Telmia-obasan" and "Ileyda-obaachan" like she does.
Vanrose
For the most part, he doesn't bother with honorifics, sticking to only first names. However, he does occasionally use -san, in the cases of Doug, Jean and Eberle, which can mean one of two things. Either he is willing to use a respectful term for someone who is older than him, or it's because they are professionals (a blacksmith, doctor and nurse respectively).
The only two people he doesn't directly refer to in-game are Telmia and Ileyda, and what he uses for them can be determined based on his reasons for using -san. If he uses it for all people older than him, he will definitely use -san for both women, but if it's due to the job status of the other three then he'd probably just use their names.
Emmy
Like her brother, Emmy is fond of using familial honorifics for the older characters; the same ones, in fact. However, as per her characterization, hers are not written with kanji, and she also uses the "o" before the -niichan and -neechan while her brother does not. Most likely, this is a result of her childish nature, being only six.
She is the only character who refers to every single person in the game at one time or another, so we know exactly how she speaks to them. However, like her brother, she very well might use the -oneechan suffix instead of -san when talking directly to Shelley.
Doug
As with Vanrose, he is usually on a first name basis for people. However, for professionals such as Jean and Eberle, he uses -san. The only other person who has the -san suffix affixed to her name is Telmia, but that could be out of respect as Philis' mother. He does use -kun for Ark after the death of Falken, but calls the youth by his first name during the final dungeon; I take this to mean that he uses -kun for more emotional moments of downtime, and omits it during times of danger.
There are only three people he never uses the name of: Ivy, Shelley and Diana. Most likely, due to this analysis, he would just call them by their names. While Ivy is also a Gate Guardian who has protected them, he (along with most of the rest of the cast) focuses mostly on Ark as the game's protagonist, so that factor wouldn't give her a nickname once he began to trust them (he only mentions his Trust for Ark, even though Ivy's fought for them as well). In fact, he only really acknowledges Ivy during the time she leads him, Halley and Emmy, and during the Big Reveal scene at the end. Plus, Ark was the only one who actually fought Falken, since the CIMA left Ivy back in the boss room when teleporting her partner to the arena.
Eberle
For the most part, she uses -san for people. The only exceptions are her family, where she uses the Japanese equivalent of "dear" for her husband and simply calls her children by name. So it's easy to pin her language usage down: if she ever had the opportunity to talk with Shelley or Ivy, she would use -san for them as well.
Shelley
She does use names for characters she's close to, most notably her three friends, however she uses -san for people who are older than her. When talking about people younger than her, such as the Gate Guardians, she is fond of the -chan and -kun suffixes.
Due to this analysis, she would most likely use -san for Eberle and Telmia, but Halley and Emmy are a little harder to pin down. Because of their extremely young age, most characters simply call them by name, even people like Rick who also employ -chan and -kun for younger characters. Whether or not Shelley would use the suffixes for them is yet to be seen, since she doesn't talk about either of them in the story, though I would guess she calls them by name like most everyone else.
Yurald
As a professional, he uses -san for practically every character in-game...including some that others would simply call by name or a different honorific. Therefore, he most likely keeps the theme up for each of the characters he never mentions the name of in-game. But like Shelley, he never uses a name for either Halley or Emmy...so it's up in the air what he'd do for them. I think he probably would just use their names since they're children, however I could be wrong on this one.
Philis
While -san is her usual pronoun of choice, she has also been known to use -chan for both of the children. There is also the obvious use of parental terms in reference to her mother, but it's the more formal "Okaasan" as opposed to Halley and Emmy's "Papa" and "Mama." Also, she is the only one in the game who calls Jean -sensei, reflecting his status as a doctor.
The only people she doesn't mention names for are Vanrose and Shelley. However, considering the way she talks to the other characters, they most likely would be referred to with the -san suffix.
Rick
His speech patterns are very similar to Shelley: -san for older characters, -chan and -kun for younger ones and names for his friends. Seeing as though he only calls Halley by name without an honorific, it's a bet he probably doesn't use any for young kids. So his speech patterns are probably reflective of hers and vice-versa.
Out of the characters he never refers to directly, Philis would probably be given -chan due to her younger age, while Ileyda, Jean and Telmia would get -san. Emmy would most likely be just called by her name, the same as her brother.
Diana
Just as with Shelley and Rick, she uses -san for people older than her, -kun for younger males and names for close friends. However, she doesn't mention the names of either girl who would be given the -chan suffix by the former two characters, nor does she speak directly about the children. So some of her mannerisms are partial guesswork on my part due to the insufficient evidence, as the only three people we hear her call -san are the same three that Vanrose specifically does...the professionals Doug, Eberle and Jean. She could have his speech patterns and just add the -kun due to her attempts at flirting with Ark, or she may speak just like Rick and Shelley and use -san for anyone older and -chan/-kun for the younger ones.
Despite this, I am going with the belief that she does use honorifics in the same way that Rick and Shelley do. Both Ivy and Philis, therefore, would get -chan, Halley and Emmy would be called by their names, and all the older characters would be given -san.
Ileyda
She is quite similar to Eberle in how she speaks, using the affectionate "anata" for her husband and -san for the rest of the cast. Therefore, the -san suffix would most likely be used for the characters she doesn't directly refer to. Halley and Emmy, however, prove yet again to be a bit of a difficulty, as she never speaks about either child so we can't see how she would talk to them in general. There is a good chance she just refers to them by name like the rest of the characters sans Philis, though the -chan suffix is still a possibility.
Jean
Though at times he uses -kun for Ark, most of the time he calls characters by the -san suffix with the exception of just using the names for his wife and children. Ark could also be a case similar to Doug: he uses -kun in more emotional moments, however -san is for times when things require action. It is interesting, though, that he never really uses -chan for Ivy, not having any of Doug's excuses, but that could be due to the fact that he never refers to her in an emotional moment.
In this case, he probably uses -san for each of the characters he doesn't directly mention (Shelley, Philis, Diana, Ileyda). There could be a chance of him using -chan for younger girls like Ivy and Philia in emotional moments, however there isn't enough evidence to prove this as a fact.
Telmia
Since Philis is her daughter, she simply refers to her by name, while the rest of the cast has the -san suffix. Like with a few other cast members, she never talks about either Halley or Emmy, so we cannot be sure of how she refers to children other than her own. She might just use their names, or perhaps use -chan like her daughter does, but there is no way of knowing that at the moment. But for all other characters that she never directly refers to, the -san suffix would probably be used.
Claude
Though he most likely speaks just like Yurald, -san for every character with the possible exception of children, the only ones he actually refers to by name in the script are Ark and Ivy (as if the poor guy's character development wasn't already derailed by simply acting on his role as conductor). Because of this, there is no way to know for sure exactly how Claude would speak about the other characters. I would probably go with the use of -san for everyone due to his professional nature, but this is another one I could be proven wrong on sometime in the future.
Pretty much all the adults in the Japanese version have occupational titles listed after their names. Nothing unexpected, but this is the best place to put them.
Vanrose: 剣士 Kenshi lit. Fencer. It fits the fact that he wields a bladed weapon.
Doug: 鍛冶屋 Kajiya lit. Blacksmith. Obvious from what he does for you in-game.
Eberle: 看護師 Kangoji lit. Nurse. Again, it's her actual stated profession.
Shelley: 剣士 Kenshi lit. Fencer. This, I still don't get. Shelley fights with a rifle, not a sword. Either they messed up somewhere down the line or she learned some techniques from Vanrose (which is an amusing thought).
Yurald: 神父 Shinpu lit. Catholic Priest. I don't even know if there are any other terms for Christian clergy in Japan which is why they went with Catholic, but his garments are close enough to not be a problem.
Rick: 手品師 Tejinashi lit. Magician. It can also mean Juggler, though it's obviously the former being used here. However, the latter usage leads to a very amusing thought of Rick trying to juggle Majesties as part of his magic show...
Ileyda: 主婦 Shufu lit. Housewife. It can also mean Mistress, but we all know it's the former.
Jean: 医師 Ishi lit. Doctor. Another whose actual in-game profession is listed.
Telmia: 料理人 Ryourinin lit. Chef or Cook. Makes you wonder if she really did own or work in a restaurant back in the city to make ends meet.
Claude: 車掌 Shashou lit. Train Conductor. Yeah...like the guy with the least character development, mostly tied to his job, would have anything else listed.
For some reason, Diana doesn't have a title listed. I dunno if the manual writers couldn't find a way to describe an unmarried housewife, or she was living with her parents before heading out to the frontier. Maybe she was planning on staying home since her wedding wasn't going to be that far off, then move in with Rick after the fact. I guess we'll never know unless they do make a sequel.
Here are other things I've noticed in the Japanese version, mostly relating to character personalities, but sometimes about little translation differences I've noticed (when it lies within the scope of my scant knowledge of the language).
1. Emmy tends to refer to herself in third person a lot. Most times when little kid characters do this, it seems to be an attempt at making them cutesy.
2. Also, in relation to Emmy, the script writer doesn't seem to use Kanji for her dialog: regular words or character honorifics. It may have to do with the fact that she's only six in Frontier Stories, thus not very far along in her schooling, even though her writing ability isn't reflected in how she speaks. Kudos for the writers for coding her lines like this...mostly cuz I can fluently Romanize Hirigana and can use software to figure out and translate her dialog.
3. Doug's starting to using the -kun suffix after the death of Falcken shows a lot about how his attitude towards Ark changes. Before, he was placing blame on all Gate Guardians for Elizabeth's death, and very untrusting of Ark, not even referring to the boy by name. Though he still doesn't respect the organization, he finds respect for Ark's abilities and desire to protect them, and begins using an honorific in more emotional dialog and his name when encouraging him in battle. Even without being able to read all his dialog, if I'd played Frontier Stories before CIMA and didn't know what was going on, I'd be able to use this to figure out that Doug had changed his attitude towards the boy.
4. Zenox (aka Genox in the English version of the game) peppers his dialog with random English phrases. For example, he is prone to crying out "Unbelievable" whenever he loses, and uses both "The End" and "Bad Ending" before and after the battle with him respectively. These words are written out in Katakana since they are English in origin, meaning one only needs to know how to sound out the script to find more examples.