There are pros and cons for either way. At FW, you will not have a themed pool. I'm not sure if there is even a water slide there. The pools are just very basic backyard pools there.
When I stayed at FW a few years ago, the transportation was horrible. There was a minium of one transfer to get to any of the parks (i.e. a bus to the boat dock, and the boat to the Magic Kingdom, a bus to the T&TC, and the monorail to Epcot). I don't know if the transportation has gotten any better there--perhaps someone who has stayed there more recently will know. But if I were to stay there again, I would definitely make sure we had a car.
The cabin will give you two rooms--you could even sleep on a murphy bed in the living room if you wanted to. You'd also have the kitchen, which would be nice for breakfast.
I like the theming at the POR, and the rooms are nice. The pool would be more fun for the boys. The boat to Downtown Disney is great, especially if you intend on spending some time at Disney Quest.
I guess it's really just what you want from your trip. Hope this helped.
Karen