Wilderness Lodge is our favorite. It just feels so comfortable to us, is absolutely gorgeous, and gives you a feeling of quiet seclusion despite being so close to MK.
We often go in the Fall and appreciate that the entire resort (with the exception of the cabins) is under one roof so you don't have to get wet to get to / from your room. We also love the beautiful location on Bay Lake, and the boat transportation options that it offers. The quick bus to MK is pretty nice too. We also appreciate that it is one of the least expensive Deluxe resorts, so you get the perks of a Deluxe resort for what can be just a small amount more than you'd pay at a moderate. We book Standard View, which helps keep the cost down as well, since some upgraded views cost almost twice as much per night for the same size room.
Among the moderates we loved POR, and found it to have many of the attributes we love about WL, with its quiet rural feel.
It is definitely a personal decision, and you can't go wrong with any Disney resort, but WL is definitely our favorite.