Not getting any easier is it ?
We have stayed at both and I love them both for different reasons. You just need to think about what are important amenities to you. Forget about the rooms. We have done queen/bunkbeds at both. Very similar. We had a WL woods view and never stepped foot on the balcony. But we did not have a view of Wishes. These hotels are so beautiful you will find yourself roaming about and enjoying them in your spare time. Unless you have a savanna room, you may never really use the balcony. I've left my gang sleeping, while I walked around both hotels rather than sit on the balcony.
Like ead79 said, same architect so very similar in style. Big differences to me:
SIZE - AKL is much bigger than WL, but don't fear the walk, if you end up in standard view, none of those rooms are far and if you are very lucky like we were to bump you up to a savanna, who cares about the walk.
POOL - AKL is much bigger because the hotel is and it is no where as pretty as the WL pool. But your kids will like either one, especially their age. Both have slides, hot tubs, games. I loved the WL pool, but it was a quiet time of year.
FOOD - AKL has BOMA, JIKO, and a good sized food court. We would only eat at the WL snack bar, the Whispering Canyon was of no interest to us and the Artists Point we ate once many years ago, and it was not a wow atmosphere. So WL food choices did not impress us. When we go back, we will just plan our meals away from hotel.
TRANSPORTATION - It is really nice to boat to MK, but we found the buses to all the rest was a long ride. Our AKL bus ride to MK was 10 minutes. It really is not that far out, just feels that way. So transportation would not factor in my decision.
EXTRA AMENITIES - WL has the watercraft, view of water parade and ability to run/walk etc. At the AKL you have the pool and the animals. So if you are a sports person this may not be for you. My DS who runs felt confined our second trip to AKL. He now requests only hotels where he can run.
ACTIVITIES - The AKL has so many you almost can't do them all. My kids loved doing them our first trip. Then a few years later and older, they aren't as interested in the activities or the animals. I highly suggest that anyone who thinks they want to stay there, do it while your kids are young or without them.