It all depends on which one intrigues you more. We have stayed at and enjoyed both resorts; each is a Disney original offering large rooms great restaurants and easy access to the monorail. Our family enjoys the Contemporary over the Polynesian with its renovated rooms and bathrooms as well as the hustle and bustle of the Grand Canyon Concourse. That however is just our choice you might find the décor and atmosphere at the Polynesian more to your liking. Go with you “gut” which one do you want to stay at more?
If given the choice, I'd choose Poly hands down. They're both super convenient to Magic Kingdom and Epcot, and both have equally sized rooms. To me it's whether you want a tropical, South Seas Theme for your vacation, or no theme at all.