Never thought about custom schedules... That is an awesome idea.
I think everything besides prime time and division games should be up to the user.
Also -
- Incentive based contracts - Brady Quinn has one of these and I think from a management perspective it would really add to the whole experience. You want to build up and progress a player but you also may want to hold him out of a starting role if you already have a decent performer. This would cause some players to call for a trade or a re-structured deal.
- Team Records - They aren't that hard to find - and they should be a big deal when they happen (489 yards passing in one game is held by Bernie Kosar, FYI)
the list goes on...