-Make storyline bosses scale to your party's level, especially the endboss. If you did all the sidequests available to you, you had no choice but to way overlevel yourself.
-No missable items or enemies. Missable quests I can understand, but don't lock us completely out of items or enemies we'd want to fight but could have easily missed.
-Make battles with enemies five levels above/below you a bit less pointless (unless you have Night Vision gems). It's like I could fight an enemy four levels higher no prob, but once they get five or six levels higher than mine, then my accuracy/evasion just falls off a cliff, and vice versa.
-The Gamepad can be used to manually use your AI teammate's arts so you can actually coordinate them outside of chain links. Can't stand it when I'm waiting and waiting for someone to use break on an enemy so I can topple it, and a character that can independently topple enemies like Melia will be tons more valuable as an AI teammate. You could make a character with a rifle cooldown ahead of time. The battle system would open up and lend itself to extra layers of complexity.
-Outside of battle, the Gamepad can display sidequest information.
-Instead of that huge ass giant webbed mess of an NPC log, PUT THE M'FING THING IN ORDER!! When I'm looking for a guy, let me spend 10 seconds finding his name in alphabetical order instead of 20 minutes going around in circles! That's what made me resort to using an online guide more than anything. Also, actually tell us more specifically where an NPC is located, rather than the general half-mile radius. Telling me NPC A is at the Ether Light region surrounded by 50 others is one thing; telling me she's at the canteen is way better.
-Even more unique custom clothing for each character. I've never played a game where each individual piece of armor really changed the look of every character.
EDIT: more
-If you're going to let the player control the time and day/night cycle again, go ahead and let us control the weather too. At least throw this in a New Game+.
-Speaking of a New Game+, let the player choose to start at level one again or go back down to a previous level.
-Option to turn off in-battle dialogue, grunts and shouts. Didn't bother me at all, but many others complained.
-Replace the giant arachnids with the cutesy spider from Super Mario Galaxy so arachnophobes like me don't have to worry about heart attacks (just joking... or am I?)