You can set them individually in next-gen Maddens. In fact, if you sign a new head coach, it resets that teams tasks to CPU and you have to go in and switch them back to user for that individual team.
As for taking out the ability to control all 32 teams, that would be a deal breaker for me. I wouldn't put my money down if I couldn't do that. That's why I've been against the whole "just put NFL Head Coach 09 as their franchise mode", because I honestly don't see how you could make that work and still have the ability to control all teams. Same with this new free agent bidding system they've announced...