We've stayed at WL in late January and June, so a 'quite' and 'busy' time of year. We never really had to wait more than 10 minutes for a MK boat or a CR boat. I think the longest we ever waited was at the close of the MK, where we had to wait for the second boat. I'm sure that was a lot shorter wait than a lot of people waiting for buses, though!
I agree the DTD bus always seems to be the longest wait, probably because it's shared with GF (or it was when I was there last). As an option, we frequently took the TTC bus, walked over to the Poly and took their DTD bus. Sounds convoluted, but it worked for us.
Overall, I would say the WL transportation is no better or worse than any other Disney resort I've stayed at, and it has more options for transportation too (boat, bus, bus/monorail, foot to FW).