It really truly depends on what you want out of your first trip to WDW. If you know that you're going to spend more time in MK, then it makes the most sense to stay at a monorail resort. Many people are wary about AKL because of the transportation issue, but I can attest that transportation to/from AKL is not an issue. I think that while AKL is far from the other resorts, the bus transportation is no different than the other resort buses that go to the deluxe resorts. We've never had an issue with transportation to/from AKL, furthermore, we like that AKL only had one resort stop- in that AKL doesn't share with any other resorts. However, now with Kidani Villages, there will be two stops, but still, it's not bad compared to the resorts that have multiple bus stops, such as BW/BC/YC that sometimes shares bus routes (it changes depending on occupancy and the season, so don't quote me) or have mutliple bus stops (SSR).
In terms of theme, we love, love, love AKL. This resort has one of the best, most unique theming compared to other resorts in the entire world, let alone WDW. I can't get over how unique it is. I loved the architecture, the decor, the whole concept. I think for my family, while the Poly is great (especially with its close proximity to the parks), the whole tropical theme is a "been there, done that." My family frequents tropical locations on business/leisure frequently so it's not something that we really care about at WDW, especially since it's a theme versus the "real thing" (please no flames- I'm comparing the Poly to resorts in "real" tropical locations, such as Hawaii and Malaysia for instance). In terms of restaurants, Poly is better situated in that there are more restaurant choices with the whole being on the monorail route thing. However, the food at the AKL is amazing. My family makes it a point to eat at Boma every trip (regardless of whether or not we're staying at the resort). Jiko is also fabulous. Sanaa's been getting great reviews as well.
Good luck deciding! You can't go wrong with either!