people around here have many different opinions, but honestly the real biggest problem with the game was, and is still, the lack of content, Its much smoother than it was, but there is a real lack of things to do in the game, the story is spaced far apart, the amount of ways to level effeciently has actually gone down. The game has added very little actual new content since release. mostly they added # big NMs 20 little nms and a bunch of side quests, that dont really feel like a story that much. thats about all.
If your listening SE content was the biggest voted missing thing i believe, realize that regardless, the battle system is an aside, some people may hate some may love it, but lack of content is what is really missing across the board amongst all players.