Squall was quite annoying when he was lost in Perpetual Angst back in FFVIII, but he apparently got over it when Tetsuya Nomura had the Heartless pwn his world, thrusting him into the plot of Kingdom Hearts. Oddly enough, both Cloud and Sephiroth found their way over there too, and a scene in KH2 shows Cloud and Squall back-to-back against an invasion force, sniping at each other as they fight. I think it qualifies as Square-approved fanfiction, complete with Sephiroth as a Mary Sue...with his long hair and seeming insurmountability in his role as an optional boss, he'll give you a good fight if you manage to figure out how to find him in each game. Just be patient, because his HP is through the freakin' roof and he doesn't give you many openings.

On the subject of characters people hate, why does everyone gang up on poor Yuffie?