As much as I would want to see the basic things above, I do not want them in for the sake of realism. Yes I want Assistant Coaches, but I have not seen a brilliant idea anywhere of how they should be implemented. (if there's a thread around here, please let me know). Even HC09 execution of GM, and Asst. Coaches was weak.... and i LOVE that game.
I would love to see realistic complex contract structures with performance incentives, guarantees, etc. however management of salary cap is a point of frustration for a lot of users. Many play coach mode instead of owner to avoid the added financial challenges. Annually there's a thread asking for cap help.
I thought I wanted custom draft classes too. Then, I realized what I really miss is porting my NCAA roster into Madden. The full player editing we currently have, while cumbersome, is really not fundamentally different than custom draft classes. You can spend a few hours doling out the guys expected to enter the NFL next year, maybe even in 2 years but after that it's a speculative crapshoot and is no further from sim than the generated draft classes currently in the game.
I agree with you on all other points.