When it comes to transportation/overall convenience, I prefer Contemporary
if staying in the tower. The walk to MK took me 10 minutes from the CR bus stop, and everything (food, shopping, transport) is an elevator ride away if you're staying in a tower room. However, the Poly isn't far behind. From Poly, you can walk to TTC (very convenient for most of the rooms), and there is a direct boat to MK (CR doesn't have the boat).
I also prefer CR's restaurants. California Grill is my favorite Disney restaurant for the food/views, and Contempo Cafe is one of the better quick service restaurants. Again, Poly isn't far behind: it has Ohana (I love the turkey for dinner), Captain Cooks (Dole Whips), and a sushi bar.
Both Poly and CR have fantastic (although VERY different) views of the Magic Kingdom. I can't really choose between the two, as they're both awesome in their own way.
As far as rooms/service/pool/theme, Polynesian wins for me. CR has gorgeous new rooms, but I can't stand the bathrooms. Service has been consistently better at Polynesian. Seeing the castle while you swim in the volcano pool is awesome (then again, the Contemporary has parasailing). And of course, the South Seas theme of Polynesian is very relaxing. Overall, I prefer the Polynesian.
Poly:
CR: