1.  The temporal physics -- Well, duh, you think I wouldn't notice the inevitable paradoxes in a game based on time travel?  For example, if Janus was dumped in 600 A.D., he'd only be able to predict what happened during that time.  How exactly would people see his prophecies being fulfilled -- 12,600 years in the past?  And that's another thing: what's up with the B.C./A.D. stuff?  If I'm correct, Christ doesn't even exist in this game, so how could they base their dating system on His birth?  And also when Queen Leene is captured, Crono and Lucca see her disappear into thin air like in Back to the Future, which is TOTALLY inaccurate.  If Queen Leene were captured and Marle were never born, Crono would never have even bumped into her at the fair and gotten transported 400 years into the past in the first place.  And what's with the chest upgrading?  If you get the one in the future, it would be stupid to get the one in the past, since the upgraded item would instantly disappear.  It doesn't matter if you took it with you; as far as the timeline is considered, it never existed.

2.  The enemy encounters -- Yes, sometimes random encounters can be annoying, but at least you don't bump into monsters every time you go into a room!  Grrrrrr...

3.  Lavos -- What kinda stupid villain is this??  A parasite that sucks up the life force of the planet (or something...what did they call the planet anyway?) and then annihilates it.  It's pretty counter-productive to destroy your only source of energy if you ask me.  And didn't he unburrow to destroy the Zeal Kingdom?  Where does he go after that?  In fact, where is Lavos in A.D. 2300?  Hrm.  And exactly what was up with the Lavos Core and the messed up dialogue everyone says before you fight it?  I don't get it...do you?

4.  The name -- What, they named the entire game after that puny thing you use to revive Crono?  What makes him so freakin' "important to the space-time continuum" anyway?  Frog or Magus could kick his sorry butt any day.  Speaking of which...

5.  Frog's Old English -- If you ever thought he sounded weird, it's because he does.  His grammar is abominable.  It gives me violent seizures.  I'm convulsing even as I type.  If you want an example of a decent attempt, take a look at Cyan's dialogue.  Kudos to the translator for not butchering it like the Chrono Trigger people did.

6.  The Entity -- The only explanation ever offered for the whole messed up time travel thingy was mentioned twice in the entire game.  What are they trying to say?  That "the Entity" is about to die and its flashbacks are making Crono and Co. travel through time?  Riiigght....

7.  The loose ends -- What in the world happened to that tree that the girl in Zeal planted, and why did the Guru tell her not to?  And what was up with that whole thing where Lavos crashes into the planet and Crono wakes up to Marle calling him "Honey"?  I played through the whole freakin' game just to figure out what happened there, and what do I get??  NOTHING!  GWARRGHH!!  RGAAAGHHH!  NWAAAHHH!  FUNGAAAHHHHH!!

Chrono Trigger rocks.