Some of the responses on this thread are laughable. From the furthest room at the AKL to the bus stop is 1200 feet or less. That's not even a quarter mile.
OP, the Polynesian and AKL both have advantages and disadvantages. Both are on the far end of the property--just different far ends. If you want to take a break and are at the AK, then getting back to the AKL will be fastest. From the MK the Polynesian *might* be faster, but then again it might not. It can take up to 20 minutes to get from the MK to the Polynesian by monorail, and it's 14 minutes from the MK to AKL by bus! IMHO the monorail is not nearly as efficient of a way to get around as people think it is.
Also keep in mind that other than Epcot and the MK, you still need to take buses if you are staying at the PR.
Here are some things to consider about the two resorts--I've stayed at both multiple times. They are both large and somewhat spread out. The furthest room in each resort from the transportation is about the same. The Polynesian is actually a little more spread out--yes folks, it might not seem taht way, but the PR has a larger architectural footprint than the AKL! One advantage to the AKL is that all the rooms are under one roof. So if the weather is bad you don't need to go outside to get to food, the gift shop, the lobby, transportation, etc.
The rooms at the PR are considerably larger. But not all of the bathrooms have the split plan. Some have the sinks inside the bathroom, which many families don't like. The rooms at the PR also don't all have balconies. None of the second floor and only some of the third floor rooms have them. At the AKL, ALL rooms have balconies with a couple of chairs and a small table.
While the PR has a large arcade and the Neverland Club, the AKL has a wealth of activities for all age groups, most of which are free. In the evening at the PR, there's really not much to do. At the AKL there's story telling, infra-red animal viewing, and at any time of the day you can explore the hotel which has the largest collection of African art outside of Africa. It's also got an amazing gift shop.
One disadvantage to the AKL is that it is somewhat isolated. There are three places to get food, Mara which is counter service, Boma which is a moderate buffet, and Jiko, which is Signature dining at it's finest. At the Polynesian you can always walk over to the GF and that opens up a lot of dining options. There is no Signature dining at the PR.
I love both resorts, but in all honesty the PR is basically a Hilton dressed up as a Hawaiian themed resort. The AKL is like NOTHING else I've ever stayed in. There is NO other resort of hotel in North America where you can wake up and look out the window at exotic animals, or go to sleep with the peaceful, low braying of the Ankole cattle. I think that the AKL also has FAR superior children's activities.
I hope this helps. Like I said, I've stayed at both multiple times and am quite familiar with them. I get the impression taht many posters on this thread ahve stayed at one or the other--or neither!--so really don't have a good comparision. If you ahve any other questions, please feel free to ask.
BTW--if you mean this Christmas season, you might not have a choice--I understand that many of the resorts are all booked up.