Both resorts are terrific, but the Grand Floridian is outstanding. I just returned from a weekend trip (Feb 6-9) at the GF, and the quality of the rooms, the attentive staff, and the sheer beauty of the common grounds place it way above any other deluxe resort. The Polynesian and Wilderness Lodge are its only rivals, in my opinion.
The Contemporary has the largest rooms on property, as well as the best shops. After the GF it houses the best hotel restaurants as well (whether you choose the GF or Contemporary, one of your dinner stops has to be the California Grill!). The monorail station inside the atrium always makes me nostalgic for my first visits to WDW in the '70s, when the Poly and Contemporary were the only resorts on property and the Contemporary was considered the flagship resort. However, the common areas aren't as attractive as the ones at the GF or Poly; and some guests even go so far as to label the hotel "sterile," "dated," and "faceless."
That's my take. Go to wdwig.com for more info. Hope all this helps!