The PC version is built off of last year's game engine mostly. EA has said that the PC version of Madden has always been roughly a year behind, so many of the drawbacks for M2000 re-appear in M2001 for the PC. The AI is somewhat lacking from reviews and stuff that I've read. I've played a couple games and it seems pretty good for a PC game. I generally prefer console versions of sports games but M2001 is nice.
However, since NFL2K2 was released, I haven't thought much about Madden. Finally, I can control my players again. PS2 owners that pick up NFL2K2 (when it's released) will discover that football on the PS2 can have responsive control instead of swimming pool physics.