In my experience, it depends on your PC. I have the Logitech Dual Action Pro (very similar to a PS2 pad), and when I had a weaker video card in my computer and set the graphic settings higher than I should have, there was a noticable lag between the controller input and the commands taking place, particularly in the kicking game. However, this was resolved by me lowering the graphics settings.
I have since bought a new video card, and I run Madden at pretty much the highest settings with no controller lag issues. Don't let it scare you from buying the game cuz you most likely won't have issues, and if you do they are resolvable.