When it comes to taking the boat - there are TWO boats: one that goes directly to MK = fast, and one that goes to Ft. Wilderness = slow. I think they tend to run the express boats during peak times only. The express boat is pretty quick. When it comes to buses, there's also some fluctuation. In certain cases, the bus might only comes every 20 minutes. I aonly stayed at WL once, and we had very good luck. Just a few weeks ago though we were waiting at AK for a bus to GF and we waited over half an hour for the bus to show up (it was around 9:30am, on an AK emh morning.) And it was a shared bus with WL, so it stopped at one of the water parks first, then WL, then GF (Where we got off) then presumably went back to AK.
One more thing to consider...If you are talking strictly going to parks, then using WDW transport is pretty easy. If you are going to another resort - esp after MK has closed (or if your return after dinner is afer MK has closed) then taking a taxi or driving your own car may be well worth the time savings.