I have quite a few in FFVII. The ShinRa Building part, and deciding to take the stairs to save a couple of fights and that annoying elevator-constant-stopping part. Then there's the whole getting the ID cards from each floor to get to the next. I didn't mind it the first or the second time, but it's pretty boring after the forth time.

Then there's the flashback with Sephiroth in Nibelheim. I hated not being able to control Sephiroth - they could have let you do that, seeing as it was only temporary.

Some parts of the Temple of the Ancients was annoying too.

Then the huge mountain climb. In fact, I think most of the story/navigation after the snowboarding mini game was long winded and boring.

Then there was that part in Kalm, when you had to help Cloud find himself in all those memories. It was highly long winded.

Maybe I have a lot of hated bits in FFVII because I've over played it? It's still my favourite...

In FFVIII, I hated the part during the festival (?) part before the attempted assassination of the Sorceress. Running around in the sewers with Zell, Quistis and Selphie was a pain in the ass.

Then there was the D-prison place... that took hours to get past the first time because I didn't know where to go.

In FFX, I didn't like the Cloister of Trials. Any of them. Every time I got to a new one, I'd save and turn it off until I was bored enough to play through.

In FFXII... that tower place where you fight Cid. And a lot of the exploration before you buy the maps.