I really like the suggestions Dream and Hzcazual made. I also would like better analytics, paticularly for defense in the form of missed tackles, QB pressures, and in the secondary. Right now we are somewhat blind on defense. If the players don't make a play, we have no idea how they impacted the game for better or worse. We can see some coverage mistakes if we open a paticular game, but it would be nice to have a more definitive ongoing record.
Dream made a good suggestion for recruiting. In addition to location which I really would like to see added, academic prestige would be another factor that would be interesting as both a recruiting tool and a potential disqualifier if GPAs were considered. Coaching system would work the same way if added - some recruits would like your system and some would not either giving you and edge in recruiting or an uphill climb. It also would be helpful if some of the confusing responses that mean nothing were removed in correspondence with recruits.
In season scouting should be more useful and more interactive.
I know this topic comes up every now and again, but I really would like to see an overhaul of the redshirt system. Perhaps add a total amount allowed per team rather than year so we have more control over building for a championship year while still allowing for a rule concerning how many are used.
Finally, it would be nice to see the resume given some additional consideration in adding win/loss records vs ranked and human opponents.