My wife and I just returned from the Wilderness Lodge on Sunday, 6/16 after a five night stay. I had read the boards with some concern, as many complained of poor transportation. I must say that we thought the transportation was GREAT. The longest we waited for a boat or bus was six minutes (yes, I timed it), and most of the time we did not have to wait much at all.
One thing to know is that the ferry schedule to MK changes both according to the time of day and the 'route' of the ferry. There are usually three boats in the 'loop' between the WL, FW and MK, and they go in opposite directions. (That is, one goes MK-FW-WL and one goes MK-WL-FW.) Therefore, you can often ask the boat driver where he is going next, and if it is not where you want to go, you can wait and get the next boat that is going the other direction. In other words, if you are trying to get to MK from the WL and the boat is stopping at FW first, just wait and there will probably be one coming from FW and thus going directly to MK. The system is somewhat confusing if you do not ask, but if you do so in a friendly way, the drivers are very accommodating and will help you out. Even if you have to go to FW first, the trip is only 22 minutes (again, I timed it).
We thought the bus service to EPCOT, MGM, AL and Blizzard Beach was excellent. There were always a lot of buses and we saw them regularly, even when we were going somewhere else. (The buses to the AKL were far less frequent.) We did not go to Downtown Disney, but it seems that this is the one problem in the bus system for WL. One other thing: we went to an E-ride night, and it seems that they are not well coordinated with the WL. Because you usually have to take a boat to / from the MK, they have some problems when the boats stop running at 10.45 (and e-ride goes to 1.00). What you need to do is take the monorail to the TTC and then get a bus to WL. We only waited a few minutes, but I heard one woman complaining that she had waited for 45!
Overall, we found the transportation to be far better than we had experienced at POFQ and POR. While we might have been fortunate, my sense is that--in most cases--people are just being a little too hard on Disney for its supposedly 'poor service.' For our money, the transportation was outstanding!