Aw man, waaay too many choices. I had to go with Hojo, mainly because he was responsible for most of the things that went wrong in FVII. He fathered Sephiroth, captured (not 100% sure if it was him) Nanaki for an experiment to mate with Aerith (ew), locked Vincent up (I think Dirge of Cerberus retcons this, but the only CompFFVII game that exists imo is Crisis Core ), was in charge of the soldiers who killed Aerith's father (what a crazy random happenstance!), and experimented on Cloud and Zack. In addition, as a scientist, he opens up the entire idea of science and it's effect on nature. In fact, I'd argue that Hojo's the main villain of the game, and that Sephiroth is just a byproduct of his work.

As far as playable characters go, I would've probably picked Cloud. I admit I entered this whole phase of Cloud-bashing for a while, but in FFVII, Cloud was pretty cool. The way he acted reminds me of Spike Spiegel; they both act like free spirits, but they both have a past centered around one character they hate intensely, and it drives them almost to obsession.

I remember Tifa being my favorite for a while (not for the boobs), but I'd have to play the game again to remember why I liked her (not for her boobs).