This is a separate problem unrelated to draft AI. Free agency reveals too much. A good offseason would include a period for rookie free agent bidding, without anymore info than we had in the draft.
On Topic: The proposed idea is too much like the old system, which allowed you to draft for speed (and other physical stats) and then train your 60 OVR scrub into a 90+ OVR pro. This isn't bad when it happens sometimes, but it was too easy in the old days to make that happen ALL the time.
A system similar to the Head Coach series would be nice. However, even Head Coach showed too much when a guy was on your team. There should be a hidden rating for Confidence or Motivation or I Love My Coach This Much or Mojo or something. The higher it is, the better the player's ratings get at that moment in the season, relative to the baseline level. The better he performs, the more he holds on to that improvement.
There just needs to be a reason to seek out certain players and to keep some guys as backups. Why do some QBs sit for a year or two? Why do some players suck for this coach and play well for that one? Do some players only respond when there is money on the line? Do some rise to the challenge of big games? What about different schemes and roles?
Madden could address this by having a Motivation (etc) hidden rating that was based on the player's situation. Assistant coaches and scouts could offer tips about who would be a good fit.
"He was a slouch in the 3-4, but he'll tear it up as a 4-3 OLB.
""You're a lot like his college coach- you can motivate him!"
"He needs a year to sit, or his confidence will be damaged."
"He's too raw to cover NFL receivers, but give him a year on the practice squad and we'll see."
"I say trade him- this guy won't play for us."
This would add some strategy to personnel decisions, and it would make your choices for assistants/scouts mean quite a bit more.