This is a hard one for me.
If I were a billionaire, I would probably never stay anywhere but the Polynesian. The rooms are great, the theming is beautiful, the grounds are amazing, the views from the rooms are gorgeous, and you've got great dining options. Plus, it is convenient to almost everywhere. LOVE.
However, since I have to work almost an entire week to afford one night there (and that's with AP discount!), the Wilderness Lodge has been growing on me a lot. It is incredibly peaceful there, and the archetecture is beautiful. You have the added bonus of being all in one building, which is nice. I love coming back to the lobby at night- it feels like a giant family room where everyone gathers at the end of the day. And the fudge brownies from Roaring Forks are to die for. YUM!
So, if price is no object, the Polynesian is my favorite by far. If we're going for best value for the $, WL it is!