I think you hit the nail on the head there. Given what happened with 1.0 I'd wager that they were faced with the options of either completely rewrite the game from scrap, or rebuild from the original code. More than likely, given time and budget constraints, they picked the latter option, and now they're in a place where that's coming back to bite them on the ass.
I suspect, only suspect mind, that it would take something equivalent to WoWs Cataclysm to fix it. Blizzard jumped on the chance of that expansion to fill in code so the core zones were capable of flight and a lot of other things like that. That is probably what Square would have to do in order to allow this game to shine to its potential.
So until they get the chance to do that, if they ever do, I agree we're not likely to see changes. But damn I would like them. I love my kitty, but I'd love her more if I could more properly display she's not a pampered house cat.