I feel what you are saying but couldn't this be accomplished using player AWR that's currently in the game? We are constantly given so many reasons for things not be added to the game but I believe the game could be greatly enhanced just by them implementing some current features, differently.
For example, your 4-3 to 3-4 LB player knowledge idea, if they linked all players on-field AWR and OVR directly to individual plays in all playbooks, I think that would accomplish what you want. These ratings would increase, in these plays, the more players are used in them and even slightly for bench players (simulating the affect of them gaining limited knowledge from practicing in that teams system).
This simple adjustment to how things are currently done would add a great risk/reward effect to playing rookies or new free agents versus playing guys who are more familiar with your playbook.
Also, they should link the playbooks directly to the head coaches and not the teams. If a teams signs a head coach without a specific playbook, like a coordinator or former player being hired as head coach, randomly assign that head coach one of the generic playbooks ( West Coast, Balanced, etc). This would add risk/reward to changing head coaches and would encourage veteran head coaches on new teams to bring in players they have coached before, that are most familiar with their playbook. This could potentially add more depth to re-signings, free agent signings and trades if the displayed player OVR, during these actions, was affected by players on-field OVR in that coach's playbook. For example, Woodley might be an 88 OVR with Tomlin/Steelers 3-4, 80 OVR with Packers/McCarthy 3-4 and 72 OVR with Giants/Coughlin 4-3. (This is NOT representing the players actual on-field OVR in the coach's playbooks but just an OVR for player negotiations)
We all have ideas of new things that they could add but with all this talk of limited console RAM and company resources, I think the Madden community would be better served by requesting adjustments to things currently in the game.