Well you have the whole Newton situation, (is there anyone left who honestly believes he wasn't paid?) though I don't know that the NCAA can prove it. But even without that, you have the HBO interview with Stanley McClover and 3 other players where they stated that they were paid. I'm not sure how much more the NCAA needs...
In Madden teams do not have accurate draft picks. For example, in real life the Browns have the Falcons 1st and 4th round picks because of the Julio Jones trade. In Madden, the Falcons will still have those picks. I'm not really sure why they can't update it. It was updated in NFL Head Coach 09.
And why would teams having accurate draft picks be a bad thing?