Battle System
Next up on the list is the battle system. Here I'll layout for you how I propose getting 2 people to fight an enemy with out an established RPG battle engine.
Lets say Link and Zelda are tramping through Hyrule Field (Which will now be maybe 10 times the size of the original Z64 one). Along the way the run into some kind of bad-guy. Your default character (determined by what you are suposed to be doing at that time, IE: Zelda would be in front if they were going to the castle, or Link would be in front if they were going into a dungeon.) would be able to use their attacks freely. When you 'Z Target' your opponent, however, Link and Zelda then stand on opposite sides of the target (for enemies only). Next: If Link is your default character, but you want to use Zelda, hammer on the 'R' shoulder button to switch your control over to her. You are now playing as Zelda, and you can go back to Link by pressing 'L'(Fitting, isn't it?). This is useful because Link and Zelda would each have their own unique weapons and magic.
Side Note: At one point in the game I'd have planned that Link and Zelda come across a special type of magic; These rare spells, called Pincir Magic, can allow the users to simutaniously attack, the type of attacks depend on the type of the Pincir Spell. On a final note, I think a really nice cut scene (FMV) would go nicely with this spell.
On to New Weapons...