The main thing is that the pass arcs are improved. In previous iterations of Madden, all throws had more or less the same trajectories. Sure, you could lob a pass, but deep out patterns were thrown on very flat trajectories (the reason why "super LBs" were such a problem). If you had a receiver running a deep out and you had two defenders (LB in a zone before the receiver and the CB playing behind the received), the QB pass would be very flat and would usually wind up in the hands of the LB (batted down or a INT). If you lobbed it, then the CB would cut in front of the route and pick it off (call that the Matt Leinart/Steve Walsh effect).
In the newer passing game, QBs throw from a variety of angles (so those deep out patterns have enough arc on them to go over the LB's head without lobbing the pass). This allows you (with a good QB) to more effectively throw between zones. This greatly expanded the available passing plays that would actually work.