I think the same factors go into it that go into choosing a room, regardless of whether it's a rental. I'm sure they are different for every person, but for me, it's about cost, amenities and size, theming, and proximity to our favorite parks, MK and Epcot.
For our upcoming trip, we considered all of the DVC properties. (GFV was not finished at the time, but would have been cost-prohibitive anyway.) We loved the size, theming and proximity of Beach Club and Boardwalk to Epcot, but the cost at Beach Club was too high for our budget, and Boardwalk seemed like a better fit for a family without small children -- we put it on the "maybe in a few years" list. We loved the location of Bay Lake Tower, but not so much the theming or the high cost, and the villas there are among the smallest (especially if you are renting a studio). The theme of AKL is gorgeous, its restaurants are well-reviewed and intriguing and it's one of the cheapest to obtain with rented points, but the location is way too remote for our liking, especially since we won't have a car with us. The theming at Saratoga Springs (Upstate NY? We already live there!), Yacht Club (again, lots of nautical decorating around our home locale) and Old Key West (spacious, but feels like the set for the Golden Girls) simply held no appeal for us, except for the SS treehouses, which suffer from the same problem of remoteness from transportation as AKL. Truly, we didn't think that any of the DVC villas were "bad," but we had to nitpick in order to whittle down the list!
So, Wilderness Lodge, which scored high on every count, won the day! We rented points for a 2-bedroom villa and can't wait to stay there in May.