The problem with the game is every team defaults to west coast style offense and a basic 4-3 or 3-4 defense. I have been doing some testing and started a my 3rd franchise a Patriots one. I changed the offensive philosophy to Spread and the defense to Hybrid multiple looks because this is what the Patriots really run. I then went in and made some adjustments to positional schemes. I changed my outside Linebackers to balanced, and my inside linebacker to Run Stopping. I also changed my 4-3 ends to balanced. The overalls all changed accordingly and my team was number 3 in defense all year.
So in my opinion it seems to be working but you have to set it correctly.