We've stayed both places, and experienced what I'd say was typical for a week anywhere on WDW property. We had great bus (and in the case of WL, boat too) service all week at each, with short waits 95% of the time, with just one random "issue" during each stay (e.g., waiting for 45-60 minutes for transportation). The "issues" were occasioned by buses breaking down or by some kind of main transportation office snafu, and those sorts of things crop up occasionally no matter where you stay.
WL has the overall transportation advantage given the boat to the MK (sadly, it no longer has a walking path to Fort Wilderness, which was nice) and the fact that it has just one bus stop, but I wouldn't consider those things to be a dealbreaker or dealmaker in choosing which resort to book.