We have stayed at WL twice. The first time was April 1997, for 5 days. At that time I had read a lot of complaints about the transportation, so we rented a car. WE NEVER USED IT! (Except to drive to and from the airport.) The second time was May 2000, for two weeks. This time we rented a car for only a few days during the trip (picked up and dropped off from the Car Care Center on Disney property). We only did this because we went to Universal for two days and because we were going to Victoria and Albert's one night and didn't want to ride the bus in our "finery." If it hadn't been for the Universal days, we would have skipped the rental car and taken a cab to V&As. The rest of the two weeks we took Disney transportation. No problems at all. I don't think we ever waited more than 20 minutes for a bus, and that was when we had just missed the previous bus.
Personally, I think the Disney transportation system works amazingly well, and it's incredibly relaxing not to drive on vacation!