From a gameplay standpoint the biggest flaw is that once you have magic, there is no sizable difference between most characters. You even get three different "berserker" style characters with Mogs dances, Gau's rages, and Umaro Umaroness. The large cast would be greatly improved if they were kept more unique during the world of ruin part of the game, and you would use different character parties for different challenges. Like Celes would be vital for a boss who would use strong spells on you.

I also love the dungeons that involve multiple parties.