We stayed at the Polynesian for our honeymoon and it was wonderfully romantic- it is a little pricey though- it really depends on if you plan on staying at the resort instead of doing the parks. If you plan to take it easy on your honeymoon and be back in time to enjoy the sunsets on the beach and the water parade or be around for the early mornings (I love that they do Mickey heads onthe sand every morning) to enjoy the resort, it is worth it. If, on the other hand, you are up at the crack of dawn, hitting a different park every day and not coming back until after the park closes, IMHO, it wouldn't be worth the extra money to stay there. Wilderness is beautiful too, just not as convenient to get to the parks (you have the Transportation Center right next to the Poly), but very pretty.
I am still amazed Disney hasn't opened a couples (or adults) only resort (like the Poconos or the Mexican resorts) for people who want that kind of experience, especially on a honeymoon or anniversary trip.