We like switching resorts. Since you are there two weeks, and will be at the parks a lot of the time, I would do a week at two different resorts. That will give you the feel of each resort, even though you may not be spending a lot of time there. Here is my take on each of the resorts (and I would recommend them all - but still I would only stay at two - then you could choose others on later trips).
Boardwalk - Love the ease to get to EPCOT and be in the countries so easily through the international gateway. Another great aspect is that it is easy to get to Hollywood Studios (either a boat ride or a walk - which isn't bad if you happen to get a DVC room over on that side of the resort). It is also great to get breakfast at the Bakery there. They have delicious pastries and a drink station there, if you happen to have the resort mugs. I also love the clown pool.
Animal Kingdom Villas - Love this resort. If you go to this resort, I would recommend a week. It has such a relaxing atmosphere, and the animals are amazing. I feel if you only stayed a few days, you may not get the great experience with the animals (as there may be times where there are not a lot of animals at the times you are passing through - but a week would make sure you would have some great experiences). I really don't think the bus service is that bad there either. It is a direct bus to every park. Other than Jambo and Kidani (both Animal Kingdom Lodge), there are no other stops. You don't share it with other resorts (as Boardwalk does) and you don't have a huge resort to make a lot of stops at (as Saratoga does). The pool at Kidani is my favorite of all the resorts (though I haven't been to Beach Club, so that may change).
Wilderness Lodge - The boat ride to Magic Kingdom is great. If you want to do Hoop Dee Doo and possibly a horseback ride, Ft. Wilderness is a short boat ride away. The pool is nice. While I really like this resort, if you were going to do the longer stay at Boardwalk and shorter somewhere else, this would probably be a good choice for the other one.
Polynesian - We just got back from a trip where we stayed in a studio with a lake view for 4 days. The view we had was from the second floor, all the way at the end of Moorea (near the TTC). While we prefer 1 bedrooms (Poly doesn't have one bedrooms), the view of the castle and space mountain from our room made up for it. Seeing Wishes was really cool from our room. There are multiple ways to get to Magic Kingdom (boat - from resort or TTC, monorail - from resort or TTC, or bus). Since the DVC rooms are on the side of the resort next to the TTC, it is also pretty easy to get to EPCOT on the monorail. The pool was pretty cool, but it got really crowded while we were there. I think I would like their pool better if I were going off season.
