I really don't think transportation is a big enough issue to be a deciding factor. Someone, perhaps it was you, noted above that it's really a wash when you consider that WL makes stops at other resorts and AKL does not. I should say it's a wash unless you are just looking at MK park. WL is obscured by trees (to give it a "wilderness" feeling...), but when you're on the boat to MK, once it goes around the trees, you can see just how close WL really is to MK.
It sounds like you've done your research on both resorts, so I'm sure you know the pros and cons of each. We stayed at WL pre-kids and are going to try it again in a few months. We stayed at AKL when our babies were 7 months old, and we will try it again in the future when they are out of strollers. We love both resorts equally, but for different reasons. We feel when we stay at AKL, we have a unique experience given the animals there. When we stay at WL, we feel like we'll be close to MK and will feel the disney magic each day. In your shoes, I'd simply choose one resort for this trip, then the other resort for next trip. It will give you a reason to plan another trip! I can't imagine your not liking both of these resorts, so don't stress over your decision. You've chosen 2 very good options.