Well, that's pretty subjective, and my guess is that you're going to get lots of different answers!
We have stayed at all three, and the Wilderness Lodge is hands down our favorite! We love the overall theme, the breathtaking lobby, the fact that it's all in one building, and we prefer the boat ride to the Magic Kingdom over the monorail. (There's nothing like being on that first boat to the Magic Kingdom on a foggy morning.) We also love being so close to Fort Wilderness and all the fun things to do there. Plus, DH and our little guy LOVE Whispering Canyon Cafe - and I would sell my soul for the Cedar Plank Salmon at Artist Point.
Also, we love all the little details - the Mickey totem pole in the lobby, Fire Rock Geyser, the music they play everywhere, the rocking chairs near the fireplace, the little bridge over the steam in the lobby, and the cozy little corners and nooks . . .
And, for what it's worth, we always rely totally on Disney transportation. We have had no problems at all with the boats or busses to or from the Wilderness Lodge. I traveled with my one year old and my elderly mother last December and we had no complaints about the busses at all - and we spent tons of time at Epcot and Animal Kingdom.
I could literally go on an on. We've stayed at many of the Disney resorts (just check out my signature) - but the Wilderness Lodge feels like "home" to us.