Separate character palettes

OR, is it possible to remove the characters from the shop screen/save menu and tweak the airship character select menu by making it dialogue driven?

You mean having a dialog box with the choice of the 14 characters + a "none" choice if you want to have less than 4 people in the party?

The event command B6 that branch on the choice of a dialog selection can only hold up to 6 different branching (so 6 characters). You could maybe ask in 3 different batches, set the appropriate event bits and you could have your 14 characters. You repeat this process up to 4 times and you just formed the party.

The party changing menu appearing is event driven (command 99) so that could easily be removed when you speak to a character on the airship. You would also have to clear the appearance bit of the NPC corresponding to each character if you select him/her.

Everything is a matter of branching properly I think.

Edit: As for removing the characters in the shop and save menu I know nothing about it.