We just got back from a stay at the Wilderness Lodge and the transportation to/from the parks was not bad at all. In fact, just the opposite was true - we never waited more than a few minutes for a boat/bus, and there were very few stops if any to other resorts.
The MK boat always seemed to be sitting there or pulling up as we walked up - luck of the draw I guess. It took less than 10 minutes to get to the MK by boat and about 5 min by bus. If you have to wait on either just factor in the wait time. The buses were pretty frequent and we did not wait long at all, ever.
Same story on the buses to Epcot. It took about 10-15 min. to get there by bus.
The bus to Animal Kingdom was the only somewhat negative experience. We went on an EMH day and the bus was packed, we had to stand, and there were tons of people who could not get on. Funny thing is, everyone waiting on a bus that morning was going to AK, there was no one waiting for MK or Epcot. Maybe we should have gotten off and gone to one of those parks!

Anyways, it was a looooooong ride and it stopped at Blizzard Beach on the way, but very few got off. It took about 20 minutes to get there I guess, but it felt like longer given it was so crowded and miserable.
The bus to DTD was pulling up too as we walked out, so again, just lucky timing. The bus ride coming back was bad though. The AC in the bus had gone out and it was like being locked in a very hot car - my son was almost passing out and we had to pour water on him to wake him up. It was horrible. Not Disney's fault, but they should not be even using a bus like that. We would have gotten off or waited for another bus, but we were pushing it with the timing to get back as we had to catch the Magical Express to the airport.
I don't think you'll have any problems with transportation from what I could tell. We had a great experience (other than the oven ride from DTD) and I had been concerned too.