We have stayed in bunkbed rooms at both WL and AKL. My DS loves them. The room sizes at both resorts are about the same unless you get a deluxe room...in this case, the deluxe rooms at the WL are larger than the deluxe rooms at AKL. I think that perhaps you would be better at WL due to its proximity to MK. Many really like the boat transportation to MK plus you can catch a bus, if you prefer.
That said, the kid activities at AKL are very unique and my DS loved them when he was 5, 6 and 7. I know WL has some but now that he is 9 he kinda turned his nose the other way. They sounded fun to me .... but ya know at 9 you have the world by the tail and pretty much know it all. LOL!
The theme is drastically different with the two resorts so take a look at which you prefer. We like both, about the same, for different reasons. We prefer the food court at WL over Mara at AKL. Lobbies are somewhat similar. Service was similar. We really liked concierge at AKL, too. Haven't stayed concierge at WL.