I love both the AKL and the Poly. But they are so different that you might be able to pick based on the differences.
Location:
* The Poly is perfect for visiting the MK - and I personally love it for EPCOT also. A quick walk to the TTC and a 15 minute Monorail ggggglide to EPCOT (the only way to truly enter Future World IMHO

. If you are going to be visiting the MK you can save a bunch of time by staying at the Poly.
* AKL is perfect for visiting AK or Blizzard Beach. Also you get direct buses to everything (you don't share with other resorts like at the Poly). If you will be going to DTD, etc this can make a difference.
Rooms (note - both resorts have comfortable, quiet rooms):
* The Poly rooms are much larger, and have true Queen size beds. How many folks will be in the room and what ages are they? If you've got 4 full sized people the Poly will be a better choice.
* You can see exotic critters out the window of your room at the AKL! Bunches of them! I was astonished at how close they came to our 2nd floor room (there is no 1st floor

. Make sure to have some morning and evening time available to just sit on the balcony and watch the fun - and also go to Arusha Rock and watch from there.
Theming:
Even though the Poly is very nicely themed the AKL is just that much better. It seemed like there was something special every few feet.
Also I have found the Poly CMs to be excellent, but the AKL CMs are even more special. Not only are they excellent, but there are so many of them from various Arican countries that you could spend an entire day just listening to their stories.
And to top it off the AKL has the best restaurant at WDW IMHO - The Boma. The good news is that you can eat there without staying at the AKL
The good news is that both resorts are excellent so you are not going to 'lose' anything whichever one you choose!