Back in the day, there USED to be separate boats to the magic kingdom from the wilderness lodge and ft. wilderness. One had a green flag, one had an orangy red flag. At slow times, they would use a green/orange striped flag to denote that one boat was serving both resorts. Then the striped flag just ran all the time. Now all the boats are shared between the ft. wilderness and wilderness lodge. However, it isn't like there is just one boat going at a time. At a given point in time there could be two or three boats going, so that there is a boat leaving ft. wilderness and another boat arriving at the lodge. So actually, it ends up now that the boats seem to arrive SOONER, because all the boats that are out are going to both resorts, rather than having to wait for the wilderness lodge boat. Also, remember that there is the blue flag boat that runs a triangle from the contemporary to ft. wilderness to wilderness lodge. This is really a nice plus for the transportation at the lodge, if you want to go over to the contemporary for a cosmic monkey or a meal.
I've also noticed them tinkering with the bus system over the past years. The last time we were there, it seems like ALL the bus routes were shared with ft. wilderness. The studios, akl busses went to ft. wilderness first, then wilderness lodge, so it was pretty transparant to lodge guests - get on and you have a non-stop trip to your destination. Couldn't be better. And, again, I think that sharing the busses means that they show up more often, because you don't have to wait for the "Wilderness lodge" bus, either one ends up at the lodge. There is also a bus direcctly to the TTC, which is just a very short hop from the lodge. The snag is the bus to epcot, which starts at the lodge, goes to ft. wilderness, then winds around the back way to epcot. To me, this seems like more of a trip than it needs to be.
It may entirely be that different routes are used at different times of day as crowd levels flow and ebb, so this may be totally innacurate to what other people experience as well.
Let me contrast the transportation at WL with say Grand Floridian, a resort that some consider the flagship of wdw resorts. The GF is separate buildings; so to go to MK, you can walk to the boat, or to the main building to the monorail. This is a wash with the boat at wl. I think the GF still shares busses with polly, direct bus to AK and studios. A wash with WL. To go to epcot, at wl just walk out, get on the ttc bus, short ride to ttc, monorail to epcot. From GF, walk out, walk to main building, get on monorail. Go around to TTC. Get out, go around, get on epcot monorail. Not that much of an advantage. So I think WL transportation is equal to any of the MK resorts; it is different than the beach club or the epcot resorts, because you are on the other side of the world; the ease of MK is replaced with ease of epcot and studios. So the comparison there is really where you want to be closer to.