I was going to post a similar observation. I have noticed that teams with players who fit their scheme better will not win a simulation as often as they should UNLESS they are the higher rated team or have the highest rated QB.
When I'm doing a dynasty with 8 or more playoff teams, I'll simulate the game in the game engine (I'll watch a football or hockey game on TV while the game is running) rather than accepting the results of the sim engine because I want the playoffs to contain the teams that are the toughest to play against.