While the entire world was epic in scope, it created a weird detachment with the character development. We had a multiple hour slog through a field with no character moments, followed by a sudden burst of discussion, exposition, and actual plot activity. The gameplay-story segregation seemed worse in this game than in any previous title. The majority of the game is just exploring around the field, and the cutscenes felt extremely discordant from that. We went through hours and hours with these emotionless combat automatons, and then suddenly be expected to empathize with them in the story scenes. I think the lack of combat instantiation actually emphasized this, as it made the combat and the rest of the world blend more seamlessly. This, in turn, made the jarring cuts between the story and the rest of the game stand out much more.
This actually isn't hard to fix. You just need to add some character interactions to help break up the endless dungeon crawl that is the world. Have character banter that triggers as you walk past certain areas, or depending on the situation in combat. Just something to make me feel like there are actually people there. I'm also not entirely sure what makes this worse in this game than in any other (since your characters are never actually "characters" on the world map in any Final Fantasy), but it's definitely there.
The Gambits need to be fixed. First, we need the ability to build and maintain multiple Gambit Decks. Since you can't do so, and changing the gambits are such a chore, you build and refine a single deck, and never, ever change it. Which results in you essentially setting up your Gambie Deck, and then never having any input on combat again, with the exception of some bosses (who are frustrating because you either have to tediously micromanage, or you have to rebuild your Deck both before and after).
This is actually one area that FFXIII improved upon. The Paradigm system is essentially a collection of different Gambits that you can switch between mid-combat. Of course, FFXIII ruined this by making the individual Paradigms have incredibly minimalistic planning and thought go into them, but the overall idea of the system is solid.
Most enemies also have too much health. A lot of fights would be completed before they really began, or effectively done in the first minute of combat because you have the correct Gambit setup to destroy them. But a lot of mobs have so much health that fighting them just becomes a chore. The bosses get incredibly ridiculous on this account. You can set up a Gambit Deck to perfectly fight 90% of them, and then you just spend a half hour watching things play out, providing no input.
While they're at it, they can remove cheap difficulty. There are two specific instances that come to mind. The first is best illustrated by Yiazmat, but it really applies to any mob with a similar ability. If an enemy can kill you, and you can do nothing to block or prevent it, that is not "hard" it is "cheap". There's no thought, no planning, no strategy. It's purely luck-based whether you succeed or not. There is no accomplishment in defeating Yiazmat, because all it means is that you got lucky. Whoop de doo.
The second instance of cheap difficulty is actually supposedly due to a hardware limitation of the PS2, rather than poor design, but since it breaks the combat system, it deserves a mention. Certain abilities are so graphically intensive that they prevent other abilities from being used. Scathe, Sandstorm, and other similar moves prevent all ability use until they are completed. They do not, however, freeze combat time. So buffs can wear off, and regular attacks can be performed, but no new buffs can be applied, nor can healing be done. This makes Baknamies one of the cheapest foes in the game, as they just sit and spam Sandstorm one after another, which prevents you from doing anything except attack, while their buddies keep attacking you. If you want to make a turn based system, fine. Do so. Turn based systems are awesome. If not, then all actions need to be able to play out in real time.