The game's linearity didn't bother me at all, besides the excellent story there were a lot of things to do. Though there were few things I didn't like:

Obtaining most of the ultimate weapons for instance, annoying and tedious procedure.

Blitzball, but in all honesty I never gave this a real try.

Kimahri was huge disappointment for a Blue Mage.

Omega Weapon, my favorite monster through entire franchise turned into some kind of joke, luckily, Dark Aeons and Penance are there for those eager for challenge.

I must be one of the rare ones who aren't bothered with Tidus voice, in fact I found Yuna's voice to be more annoying.