I think you mean ANTAGONIST dingus.
Cloud was clearly the protagonist. Definition: 1. the leading character, hero, or heroine of a drama or other literary work.
I don't see how anyone else in the game could be considered a protagonist.
As far as who the real antagonist is, it's clearly Sephiroth. Early in the game it's Shinra, but Sephiroth eclipses them pretty quickly. I guess it could be argued that Jenova is the antagonist since Sephiroth is essentially a reincarnation of her, but that's really a technicality.
If you want to get even more technical, Hojo is responsible for creating Sephiroth, and Shinra is responsible for Hojo. So Shinra is the main evil (although Jenova came long before them). But that's not what an antagonist is. Sephiroth is the main source of drama and conflict in the game. He is the one that the story follows and that it is your ultimate goal to defeat, so he is quite obviously the main villain of the game.
What the hell would the "other" option be? Cloud's subconcious? I guess you are fighting against his weak will the whole game since his stupid ass manages to hand Meteor over to Sephiroth.