I had some suggestions that I didn't want to forget or misplace.
Add Targeting in as a penalty. This will mean needing to have a disqualification mechanism, too. It would be interesting if Targeting was reviewed before it became a permanent call.
Give users the option of how to break ties in standings. Allow different factors to take precedence.
For bowl games, allow Playoff games - Quarterfinals (and Semifinals) - to take designated teams OR best available. It would be great to set up an 8 team playoff to take 5 conference champions and then 3 at large teams.
Other people can feel free to post suggestions/ideas. I will also add more as I think of them. Overall, I think the game is amazing fun. I would just like to help improve it, if I can.