FFVII:
Better character graphics. I don't understand why they didn't just use the graphical renditions of the characters used in battle sequences. Even those would've been much better than the goofy pieces of crap that are used in most of the game. It's hard to get wrapped up in the serious and deep atmosphere of the game when all your characters are 2 foot tall creampuffs with dots for eyes, especially when they stand out so starkly from the more realistic background of the game.

I frankly don't like the Materia system. Mostly because I dislike the idea that you can only "equip" magic, but never really learn it.

Either tie up the lose ends of the game, or cut them completely. Why would you leave so many things in a game that were never flushed out completely, especially things that might tie into the main storyline. I understand that it happens in lots of games due to budget or schedule constraints, but if you aren't going to finish some element of the game, don't leave half of it still in the game to confuse and upset people.