If it were me, I'd go for AKL. We hope to stay there someday. We love WL, but hope to stay at AKL in 2008.
As far as transportation, AKL doesn't share busses with any other resort, so it's direct to/from everywhere! That counts for a lot.
And keep in mind that the WDW property is pretty huge, so no matter where you stay you're going to be doing a bit of traveling.