The problem with defense, at least in the secondary is as CB said, DBs running the routes better than the WRs in many cases, or having the ability to cover both a short out route and a intermediate hook/go route. There are far too many recoveries by beaten DBs (and by recovery I mean the game engine deciding the DB shall have an INT and then boosting/teleporting them over to the ball faster than they should be able to go.) With linebackers, the problem is the MLB/ILB being able to deflect/intercept the ball 99% of the time when facing the QB with passes that go to the seam. In the NFL this is more like 10% of the time.
The real solution is to add a better physics engine to simulate the real-world acceleration and weight of players.
Edit: The passing cone in its old implementation I think didn't work, but the idea they were going for made a lot of sense.