The Chef has the right idea. Cloud is the Final Fantasy character; if you asked a hundred people which series protagonist was their favorite, you'd get a handful of responses each for Cecil, Terra, Squall, and Tidus, with the majority of the responses being Cloud. Picking another Final Fantasy character for a crossover fighter would be like picking Raiden instead of Solid Snake or DmC Dante instead of classic Devil May Cry Dante.
To Nintendo Nerds, he's not! The Job Classes are the faces of Final Fantasy!
The thing with Cloud is that he is the manifestation of SQUARESOFT'S flipping the bird at Nintendo at 1996-1997 just for not using CD's at the time. Ever since, there has never been a major SQUARESOFT(now, SQUARE-ENIX) Title on a Nintendo Console(Handhelds notwithstanding). All on Playstation! Not the mention that Cloud himself was(is?)considered responsible for the many JRPG Protagonists with ridiculous weapons, shoddy clothes, and unlikable personalities(what most fans say).
That's why some don't like him.