I've stayed at both and although it was fine and a beautiful lobby, I did not enjoy Wilderness Lodge. I think I was put off most by the long hallways to our room. I know that is a vague reason.
I did ,however, really enjoy Animal Kingdom Lodge (and we were just in a standard room). The bus transportation was fine. I never once thought "this bus transport bites". Plus, AKL just has a more "fantasy" feel to it - that Disney Magic.
Of all the hotels I've stayed at on property, for me I rank them this way:
Polynesian (especially concierge, but that costs too much now)
Contemporary (ditto on concierge)
Animal Kingdom Lodge
Swan
Boardwalk
Yacht Club
Wilderness Lodge
Riverside