I think they were all good concepts but failed execution.
I thought the battles were fairly balanced pre-Eternia, but then battles after Chapter 5 were generally annoying and I turned the encounter rate down to 0%.
I don't like the idea that Airy is the villain, in fact, it calls to question where the hell she came from to begin with. More or less, I disliked how she fit into the stereotypical role of "cute animal/companion in your party" and she ends up being the mastermind, it doesn't feel like a good use of stereotypes.
Not only is she the villain, but she's a lackey to Ouroborous for some reason. Why not just make her the main villain?
The changing of the title screen was way too cheesy.
Parallel worlds is another great concept with horrible execution. It seemed like they wanted the Celestial Realm to be the area where we real people live, but it didn't pull it off. It's nice that they used cute tricks like using the 3D camera to take your picture at the end and display it in game, but it just doesn't make sense if you try and think about all the worlds like that, because then there are now multiple Ouroborous if you consider other people's games.
I'm all for simple stories too as I often defend FF1 in this thread, but it's when you try to complicate yourself that you run into trouble. They should've just kept it simple.