Hello Elizabeth,
This is such a tough question to answer; the resorts are so different in style, but still filled with Disney magic!
First, let me share with you that if room size matters the Contemporary Resort's rooms are 394 square feet, the Polynesian rooms are 415 square feet (there is some variance with the rooms), and the Wilderness Lodge rooms are 344 square feet.
One of the perks of staying at the
Contemporary is being able to walk to the Magic Kingdom; no waiting for transportation. Overall, though, it is probably the least themed of the resorts.
The
Wilderness Lodge will make you wonder if you have left Florida; I personally adore the theming of this resort. However, the transportation to/from the Magic Kingdom does take longer as you'll need to rely on water taxis.
The
Polynesian is also richly themed and offers the best transportation options of any of the resorts, in my opinion: monorail or water taxi to Magic Kingdom and monorail (via a short walk to the Ticket & Transportation Center) to Epcot. It is also the only resort of the 3 you are looking at that offers a zero-depth entry at the pool. One drawback, however, is that the resort consists of many buildings while the other two are essentially one large building (consider the possibility of rain).
So I've shared a few pros/cons to help you make your decision. You may want to explore all the photos in the above links to see which style you prefer the most since that really varies from person to person and then which pros/cons would affect you the most. Either way, they are wonderful resorts that will I'd highly recommend.