We've stayed at both resort, in fact we stayed at both resorts during one of our trips.
While I loved the Wilderness Lodge and would love to stay there again some time, my all-time favorite Disney World resort is the Polynesian
We're a family of 4 (DSs are 19 1/2 and 16 1/2) so the larger rooms with 2 queen beds plus a sofa bed are much better for us. When we stayed at the Wilderness Lodge, even though we had a bunk bed room, the bunks are pretty small so it was rough for my teen boys to fit. Length-wise the bunks were ok, but they're very low to the ground (probably for safety reasons) and the bottom bunk doesn't have much clearance from the top bunk. My older DS basically had to slide into the bottom bunk each night because there was not enough room for him to sit up in the bed. If you have no children, or small children, this wouldn't be an issue for you.
The Polynesian has direct boat access to the Magic Kingdom (it goes from the Polynesian directly to the Magic Kingdom, and on the return trip it stops at the Grand Floridian, then back to the Polynesian), in addition to the monorail. In fact, we use the boat most of the time to go there and we only use the monorail if we happen to already be in the Great Ceremonial House.
Also, the Ticket & Transportation Center (TTC) is a short walk from the Polynesian resort which gives you quick access to the Epcot monorail.
You have the convenience of being able to watch the fireworks show "Wishes" from the beach at the Polynesian resort, as well as the "Electrical Water Parade" which passes right by the Polynesian beach each night.
The rooms at the Polynesian are among the largest on all Disney property, as far as non-suites go. They've all been recently refurbished, although I believe that the Wilderness Lodge has been recently refurbished as well.
My favorite WDW restaurant is located at the Polynesian; the Kona Cafe.
You really can't go wrong with either resort, but I recommend the Polynesian!
If you want to see my pictures of both resorts, just click the link below in my signature to get to my web site, then click on the "Disney World Trips" link to get to the resorts.
Have fun, whichever you choose!
