Well for me there were a couple of bits... I didn't really like the bit in the desert under the Gold Saucer... thought it kinda dragged on a bit and wasn't very exciting.
I also wasn't hugely keen on the first trip to Costa del Sol on the boat.. felt weird for some reason
But the bit I really didn't like was the place with the Phoenix! That little battle thing sucked :\
Still da best game ever, though :P