Contemporary!! Once you stay there, you'll never want to stay anywhere else. The view is incredible, the best on property. You'll want to spend your vacation sitting out on your balcony. I really cannot stress it enough to people how wonderful staying at the Contemporary is.
I've stayed at the Polynesian, too. The rooms are the same size and have also been rehabbed, so there's no issue there. But I think the food court is going down for rehab and it's no fun to stay at a resort when the food court is closed. Also, at the Poly, if you need to go to the main building, you have to walk outside. This can be not fun if it's too hot, too cold, raining, etc. At the Contemporary, it's all inside one building. Plus, the monorail is right there.