We prefer the Polynesian to the Contemporary. Riding the monorail to MK is quick, only one stop at the GF. Coming back you stop at the Contemporary then the TTC. Either way the monorail trip is pretty quick and easy. When going to Epcot from the Contemporary you have to ride the resort monorail to the TTC, then transfer to the Epcot monorail. From the Polynesian you can do the same, or just walk to the TTC and get on the Epcot monorail.
Other than transportation we love the Polynesian theme. It is like having two vacations, one at the parks, and one at the Polynesian. The Contemporary just reminds me of a nice hotel. But, many love the Contemporary, and the walk to MK is convenient. We just fell in the love with the Poly and can't imagine staying anywhere else.