Been to both. The housekeeping during my stay (quite a while ago) at the Polynesian was terriable. The room was nice, but nothing to write home about (this was before the renovations). I loved the concierge lounge though and the offerings. Very relaxed. Loved the themeing of the hotel. I preferred the Polynesian. Access to monorail great.
Yacht Club had a better room (cleaner, more upscale..but also a little "stiff"... lobby no fun to me - I like the Polynesian better.) the Raved about pool was ok , but not worth paying a lot more for or stressing over where to stay , etc... unless you are going to spend a lot of time there with little kids.. The Concierge at the Yacht club was VERY crowded during our stay. I think I preferred the offerings at the Polynesian -
All in all, I give the Polynesian a better score - it is one I'd like to go back to where as "I've tried the Yacht club and that was enough".