Exactly! And actually, Madden does a terrific job of portraying this sort of thing. Change the Bills back to a 43 scheme and go with a different setup (receiving back or speed back) for the RB slot (for McCoy) and they are a terror.
You're right about one thing though....players should dictate scheme. I go back to the Andre Ellington or Leveon Bell examples and their specific skillsets do not complement the scheme. In Arizona's scheme, it actually mimics real life (which is why David Johnson gained more playing time as the year progressed). However, I'd argue that there is no way that the Steelers scheme should have the RB slot set up to receiving back.
The one thing I'd like to see next year is a more careful focus by EA on how they assign position schemes for each team. For the most part, they're pretty good....but there are some pretty egregious examples where they aren't, and those teams tend to be far easier to beat than they should be.
Edit: and if you give the fantasy draft a shot....set your scheme first however you'd like it for your team, and then let the CPU draft for you....it actually makes it quite interesting