Well regarding players cut or retired after the end of the season...I'm assuming that they're leaving it at end-of-year-rosters, because that's the 2014 season roster.
In terms of other stuff, I think it's done in part for balancing. Jason Pierre-Paul has always lined up against the LT for the Giants but is more built to be on the other side, which is where he plays in Madden. Damontre Moore was not a starter at all this year, but an earlier version of the roster benched Kiwanuka and put him playing out of position (now, Wynn has that spot, and Moore is JPP's backup). When Schwartz was playing, he was lined up at RG, despite the fact that he only played RT this year because when he played Justin Pugh was hurt. I could go on and on, but if I were to guess, as I said, most changes were probably for balancing.