I am not going to add what others have already stated (e.g. injuries, keepers with magnetic hands), but have the following, hopefully constructive, comments.
3D engine just seems poorly optimised, I have an up to date graphics card (six months from new)and drivers etc, with 2 gigs of RAM. This manages to run modern games such as Far Cry 2 at reasonable resolution and detail, but the 3D engine runs like a dog. It's not as though the game is chucking out gazillions of polygons with fancy shaders and particle effects, to be frank its roughly equivalent to a SNES era Pro-Evo.
The number and variety of animations leaves something to be desired. The animations are often out of sync with the ball movement - see goal kicks as a prime example
Players spend way too long on the floor after slide tackles, often resulting in chances
Passing, especially on the ground, looks odd, players seem to hit it at a hundred miles an hour with no visible drag or friction on the ball.
Corner takers manage to walk through the six foot high advertising hoardings prior to kicking the ball
OK, that's all folks. Other than the 3D things seemed to have improved (other than Everton not having a pot to Pi55 in, but I think I should probably blame Bill K for that rather than SI ;))