I'd vote for the 4 nights Pop/3 nights WL or AKL split instead. I actually like the Contemporary, but agree with the others that 2 nights is not ideal, especially considering you'll be traveling on the other side of that second night stay. By the time you'd check in, you'd have a day and a half to really enjoy it, most likely.
WL would be preferable for the proximity to the park and seeing the Electric Water Pageant from the beach at night, if you wanted to. The suggestion to visit Fort Wilderness is a good one, too. I do think kids at that age would love AKL, though. Not sure if you'd be able to swing a savannah-view room, which is considerably more money. Of course, the boat transportation from WL to MK is worth thinking about, too. It's a lot more fun than a bus!
One other wrinkle is that the Skyliner will be closed for refurbishment from January 22-28. Not sure if that coincides with your stay at Pop, but it would be a shame to miss out on one of the main benefits of staying there.
Good luck deciding! I hope you have a great trip.