I don't mean Memoria, that's a really cool final dungeon, really high up my list. (Side note, it's been a while since I played Ultimecia Castle so if I returned to it today I likely wouldn't be able to beat it, fortunately I recorded a playthrough of that level, minus Ultimecia herself)
But I mean about what Kuja and the IIfa Tree did to the world map of Gaia. For three reasons, all of which Magemasher pointed out and I agree with him.
First, the whole planet is covered in Mist and doesn't look nearly as lovely as before.
Second, the usual theme song is gone.
Third, and worst of all, at least half of the locations become unrevisitable as the Iifa Tree's roots block them. As if Evil Forest, Cleyra, and Terra being unrevisitable wasn't bad enough, now a lot of perfectly good areas are blocked off, which wasn't really necessary, the vines could have apepared anywhere else other than blocking locations. (I can't remember, do any of those locations have Stellazzio?) This is the second worst FF game about having unrevisitable locations, first being FFXIII. At LEAST one of them isn't Treno, my favorite location.