I don't think Cloud and Tifa had sex in the game.

Anyway, I understand that Hojo is sick and probably has some weird in his head. But he never said anything about having Aeris and the dog mate. He referred to helping endangered species, but trying to /mix/ species isn't exactly the same as saving endagered species. /If/ he were trying to mix species, then logically he would know about genetics. If that was the case and he was trying to rescue a species, cloning would be a lot more efficient than hybriding, amirite? So I don't exactly buy the thing about him trying to make them mate. The whole situation still doesn't make a lot of sense to me.