The things about Fort Wilderness that made my stay just so-so were the transportation issues and the pool. I've stayed at many different Disney resorts, including ones on the monorail line and ones that just run buses, and have never really had major complaints about the transportation--but Fort Wilderness is a bit ridiculous. For instance, from our cabin we had to take one bus to a different bus stop, take another bus to yet another bus stop, walk about 500 yards, and then take a very slow boat, all to get to Magic Kingdom. I understand Fort Wilderness is large, but you would think that they would at least have a bus that went directly from the main bus stop to the Magic Kingdom, which apparently is not the case.
The pool was just gross. It was large but was just a rectangular pool, no slides or anything, and there was a film on the top of the water that was obviously a mixture of suntan oil/sunscreen and who knows what else. It didn't look as if it had been cleaned once all summer (we were there toward the end of July). Also, there were a lot of unsupervised children running around, despite the fact that it was late at night when we finally did go to the pool.
Overall, if you're going to Disney during an off-season, I think Fort Wilderness is an okay place to stay if you have no other option, but I certainly would not suggest staying there during a busy season. You waste too much time trying to get to the parks and the busy seasons tend to be warmer anyway (except for Thanksgiving/Christmas) so you would of course want to swim, and I don't suggest the awful pool here.