We have stayed at both resorts and I would give my personal vote to AKL. They are both very similar (designed by the same architect), but what AKL offers that WL does not is the animals.
Neither resort is on the monorail so therefore, I feel they are sort of isolated from the parks. I know others feel AKL is much more isolated, but they are about the same to us (we usually have a rental car and use it mostly for our transportation). About the only other connection other than busses and cars that WL has to the parks is a boat.
I also give a small edge to AKL for having Boma restaurant.
Since they are so similar, to us, it comes down to the view. To pay for the best view at WL, you get a view of a fairly noisy pool. To get the best view at AKL you can watch all the exotic animals anytime of day (and night). Even if you don't have a Savannah room, you can view the animals in tons of different places. It is really fun to do, and a very unique hotel experience.
Just my 2 cents! I'm sure you will hear from fans of both resorts, so it will probably be a tough choice to make!