A few questions if you don't mind me asking.
One, will you have a car on your honeymoon?
Each resort has great transportation, but from the research I've done it sounds like the AKL can't compete with the BW b/c of it's water transportation. And I say this grudgingly b/c I'm not a fan of the BW at all. If you don't mind buses though the AKL has an excellent and quick system. Now if you have a car on your honeymoon that makes it so much better b/c you don't have the X factor of needing to be close to everything b/c you can just hop in your car on your own schedule and drive there.
I would steer away from the CR. The only reason I say this is because it doesn't strike me personally as very appealing. A lot of people LOVE the CR however, but I don't see it as very romantic. Thats also the reason my family and I have never stayed there, sure we've explored the place and it's VERY interesting, but just a bit too busy for a honeymoon. However, here they offer thigns like parasailing, water activities, and Chef Mickeys. I personally don't care for Chef Mickeys, but a lot of people LOVE it.
The AKL sounds wonderful, but I'm a bit biased b/c we are spending half of our honeymoon there as well. I let my husband pick it out because he has not been to Disney as many times as I have and he was excited b/c one, it was more secluded, and two, what could be more romantic than seeing animals from your balcony while cuddling after dinner? Thats our take on this resort. The downside is the lack of water activities there, but for us that is not a big deal b/c we are spending the first half of our honeymoon at the Caribbean Beach and will have a chance to there. However, if water activities are important this would not be the best choice.
It seems that WL lovers generally like the AKL as well. I guess they were designed by the same designer? Not 100% sure on that though. But the WL seems very charming as well and you have water activities there, along with that rustic atmosphere. I've never stayed there though so I'll let someone who has fill you in on that place.
Is the Polynesian an option? I've stayed there a few times and it's VERY magical, though not my husbands tastes.
Best of luck with your decision making and happy honeymoon!