I prefer the AKL over the Poly...But, my kids are now 14 & 10. With a little one I would think the MK will probably be your main Park and therefore the ease of trips back to your room would definately favor the Poly.
Both are themed nicely, but the draw of the AKL is the animals. At 2, your child will not appreciate this (even though he may like seeing them). AKL is more subdued and really they attempt to make it a more quiet, serene if you will, environment. Noisy or unruly kids, for example, stand out (not in your son's age group though, obviously).
In the final analysis, either Resort will impress.