Phil told us this awhile ago and every year there is this same debate.
I've tried and tried to find the link but in the drivel in the Madden forums I have never been able to find it (it was in 08 I think).
We lost them at the conversion from old gen to new gen and I'm fairly certain it was because of how the uniforms were generated. Instead of creating just two sets of pro bowl jerseys they would have to create 32 sets.
To you and me it may not seem that difficult, but I dont pretend to understand programming and never will.