I've stayed at both resorts in the past year (!) and my vote was for the AKL... I loved the Wilderness Lodge, but the Animal Kingdom Lodge just felt like even more of an escape from reality!
Dining: I loved going to Boma for breakfast in the mornings (we did it three times - food was amazing there), and I preferred the selection at the Mara for quick service. While Artist Point is my favourite restaurant on property, I would still give the edge to the AKL in terms of food options (and no, it's not all African...).
Transport: A lot of people think that the AKL is too far away, but I've gotta tell you, that dedicated bus service goes a long way towards making the transit times equal for the two resorts. In fact, I find that the bus service for the AKL is far superior to that of the WL for getting to all of the parks, INCLUDING the MK.
Layout: DH and I had a room in the boondocks of the AKL when we stayed there, so I will give the WL much better marks in terms of layout. Next time, I'll be sure to request a room that is closer to the lobby. But, the view of the animals from our room was far superior to the one that my parents had and they were closer to everything, so I guess it's a bit of a trade off...
Theming: This is where personal preferences really come into play. I loved both hotels and I would give them equal marks for the theming but for different reasons. The WL has a homey, comfy feel to it, wheras the AKL, while still comfy, is much more exotic. I prefer the AKL because of how unique it is (especially in all of the details) and I also think that the rooms are better laid out at the AKL too. But, again, this is where personal preference really comes into play... That's where you're going to have to do your own legwork!
But the AKL's clear advantage... THE ANIMALS!!! I would wake up, stumble over to my balcony and watch the giraffes have their breakkie while I had my first coffee. Honestly, when I need to go to my "happy place" for whatever reason, that is the mental image that comes to me. And that is why the AKL will always be so special to me!!!
Hope this helps - enjoy your planning!!!!!!! (It's always my favourite part... aside from, you know, actually being there! :lol: )