Ultimately, I would have to say amenities, but part of our resort decision has to do with what time of year or type of trip we are trying to experience. Like my husband works at a zoo and really likes animals, so if it is his birthday or something special for him, I will try to stay at Animal Kingdom Lodge for the animal views.
If we are taking a quick trip and trying to be on the cheaper side, we will stay at POP. Last year for Christmas, we did a split between AOA (wanted to see it, but we didn't really like it all that much) and WL for all the Christmas atmosphere. We really enjoyed spending Christmas Eve and Christmas in the rocking chairs right outside the room overlooking the Christmas tree in the lobby. However, I agree with the room not being all that great. It felt very small and the bathroom was very dark. I could tell a huge difference between that room and the ones at Animal Kingdom Lodge.
Last October for my birthday we stayed at the Boardwalk again. We didn't go to the pool or anything, but we really enjoyed the short walk to EPCOT. The buses can be a problem there, but for the F&W festival, we usually end up at EPCOT most nights and it was nice to walk or catch the boat back.
For out tenth year anniversary, we are staying at Grand Floridian this May (although I did add a night at the POP since we decided to arrive late the night before our anniversary). I look forward to seeing the resort after this past year's renovations and am hoping that the monorail is back to normal working hours. Now with most of the resorts going to just white sheets and foot runners, it may not seem as "old" in the rooms.