Well some of these suggestions have been made already, but since they are good and I have thought these would be good additions to the game before I read them, I will repeat them in addition to my own suggestions.
1) I would like to see backups have more functionality. A backup running back with solid yet not specific ratings should be able to backup both the fullback and tailback. This applies to defensive backs, linebackers & defensive line as well. Why should a backup be limited to one position?
2) Changing positions is too heavily penalized. Players change positions frequently in college. They change from outside linebacker to inside linebacker, safety to outside linebacker, cb to safety, WR to tight end. Sometimes we see tackles become tight ends, defnsive linemen become offensive linemen and vice versa, and RBs become cbs. Kickers often punt and vice versa. While I agree there should be a penalty, it should not be so large that the player is far less useful, especially if it is done early in the career (freshman or sophomore).
3) The addition of individual coaching minutes to the practice plan would be excellent. Coaches often spend time with individual players to improve their game. Obviously time is limited, so make this one player per week (or add some other safeguard to limit the coaching minutes spent in comparison to team plans). This would allow coahces to develop a superstar or address the weakest link on the team. More customization makes for a more interesting game experience.
4) Formation packages would be excellent although I do understand the issue with fresh offensive line. Nevertheless, more control of personel in paticular packages, especially for defense, would be a welcome change.
5) An option specifying when to go for it on 4th down would be useful. If you have an unreliable kicker, and you are in your opponents territory, and you set it to avoid long field goals, you often end up punting. In this situation, going for it could be a much better choice...
6) If there are multiple players who have you as their number one choice on the final day of the signing period, why does the assistant coach seek out inferior players to sign when recruiting money runs out? I think this should definitely be changed. In some cases, where there are three schools in the running, it makes sense to lose the player. However, when only one school is listed and it is the playe'rs only choice, why can't the assistant coach be relied upon to sign that player? I think this is something that should be changed. In addition, perhaps instituting some sort of walk on system to eliminate the assistant coach from signing bad players would be a good idea. In this scenario, the assistant coach offers prefered walk on status instead of a scholarship. This way, no scholarship is resinded later and coaching reputation is not hurt. If we have to get stuck with a couple bad players while learning the recuriting ropes, we should have the option to cut them without being hurt by it. Walk on players should be expendable, just like they are in real college football. This still keeps the penalties intact for resinding scholarships though which is a good feature outside the above quirks...
7) I don't think players who do not appear on the depth chart should play.
Keep up the good work and sorry if I echoed suggestions already made. :)