In my opinion, this is the biggest problem right now. Season after season is won by teams using this exploit, with teams refusing to use it having no chance.
Here's my idea. It would not be realistic to hit physical stats, but... Play knowledge should be attached to how many times a play is practiced or used in game ONLY at that position. If a player is practicing at WR, he gets no play knowledge at RB for that practice.
If that's too hard to implement, a severe play knowledge penalty could serve the same purpose. A WR playing RB... 70% (or so) loss in play knowledge.