Tidus, Yuna, Seymour. Those three ruined FFX.

Yuffie had her annoying moments, and while I don't think "annoying" is the right word, I really didn't like Aeris much in FFVII. I liked Aerith in Crisis Core, though! Go figure. Speaking of Crisis Core - Genesis, oh man, he could get annoying.

Hope isn't as bad as any of the above, but he still has enough moments to make me consider him as "an annoying character".

Cloud is annoying in every VII sequel/prequel because they turned him into a generally wussy or depressing character. Ugh. I liked him so much more in the original game. So, so much more.

I didn't mind Zell so much, but Irvine annoyed me on occasion.

Eiko could be very annoying at times. I guess I just don't like kid characters in main parties, really.

Oh, and Krille. Get the hell out of my FFV and give me more Galuf, dammit. ;_;