1) The invisible walls. Yes I know why of their presences, but still a pretty annoying thing.
2) Not being able to do many things while in Queue. 2 years in and I can't even queue with my chocobo out?
3) Tanks being vit focused only. Being the only class that REQUIRES 2 stats (STR and VIT) in terms of being BiS, I wish that they'd simply make Vit their only stat and make STR useless.

I have many more but these 3 are the thing that pops in my mind