Hi Meredith,
Firstly, congratulations on your upcoming honeymoon. My Husband & I just visited Walt Disney World last October for our honeymoon.
This is a tough question to answer as I absolutely love both Disney's Polynesian Village Resort and Disney's Yacht Club Resort.
Both Deluxe Resort hotels are beautifully themed with similar amenities and recreation on offer.
I guess that it really comes down to location and as there will only be the two of you, I think that I would personally opt for Disney's Yacht Club Resort and here's why:-
1/ It is possible to walk to both Epcot (via the International Gateway) and Disney's Hollywood Studios from this hotel.
2/ Stormalong Bay (the pool at Disney's Yacht Club Resort) is arguably the best pool on Disney property which comes complete with a sand-bottom and lazy river.
3/ You are ideally located on
Disney's BoardWalk which offers great nighttime adult entertainment at both Jellyrolls and Atlantic Dance Hall.
4/ Being located in such close proximity means to Epcot means that dining at any of the restaurants in the World Showcase is really easy and convenient.
I hope that this information has been of help and rest assured, no matter which Disney Resort hotel you choose, you are sure to have a fantastic time.
Wishing you a magical honeymoon filled with memories which will last a lifetime!