-scrolling to find an ability to use. Later in the game this can be stressful when you have to get a critical spell off quickly. Not sure how you could improve this, as better UI still makes it tough.
-Cutscenes got tiring and took a lot of time. being able to skip them would be cool. making them shorter and adding extra interaction (ala mario rpg) would be even better.
+Materia system was lots of fun. not sure i can complain about it really.
+Limit's and getting positive feedback for taking a beating was cool, although some of the limits were just useless, which was not cool.
-some spells were useless, making battle dynamics robust enough to give every spell meaning would be a nice thing.
-turn speed... not knowing when an enemy had a turn ahead of you or not adds the wrong kind of mystery to the battle system imo. minorly random enemy turn speed might be cool.