1. It was more than a few. They had the A-10/CAA, Big Sky, Missouri Valley, Ohio Valley, Southern, and the Southland in addition to the HBC's and the Ivy Leagues. You're a Lehigh fan so the Patriot league wasn't in so maybe that's where you got that assumption? They had a lot of FCS teams.
2. They never had real stadiums on the PS2 version (maybe on PS1). I think generic stadiums would be fine to start.
3. You may be right, but they had them in previous versions. They may also be able to attract fans of FCS schools and fans' interest in general. Playoffs too maybe. Just throwing that out there.