Well like I said the game is not perfect but I only play offline franchise only so I simply do not abuse the flats. To be honest though if you wanted to you could abuse the flats with the patches just as much. One of the problems that I see with the flats is the game has a lack of true man lock meaning that the defender who is supposed to cover the back or worse yet the TE is not lined up over them or anywhere near them. So you LB is completely out of position before the play begins and if you or the comp fires the ball to the flats quickly the defender has not had time to catch up. You can really find this issue if you run the 3-4 and use some of the different blitz packages.
How about when you come out on 1st down with 3WR set but called run and the AI lines up in base formation and nobody covering your slot WR? Most of those plays are designed for the Safety to cover the slot and in a real game the safety would have lined up in a position to do so. However in Madden post or pre patch you can simply formation audible to a pass and hit the slot WR quick for about 10 yards since the saftey is about 10 yards out of position. So again the issues are there with or with-out the patches and the player has to limit themselves from abusing the errors in the AI no matter what. I just prefer the game with out some of the dumb stuff the patches produced, mostly the running glitch where your player clearly freezes for a split second but nobody else on the field does and the outrageous sim stats for rushing and sacks.
I designed some sliders based on the first 24 pages of
Breaking Down Sliders... How They Really Work which gives me a good challenge and mostly realistic games. I actually lose more games now than I was with the patches. Which to me is a good thing since I like to start with weak teams like the Browns.