There are so many great things to do at WDW for honeymooners.
-Book some romantic dinners. Victoria & Albert's is obviously the cream of the crop, although it is definitely pricey. I would either pick up a dining guide book or poke around on the internet to read what restaurants would best fit your interests. Some of our favorites were California Grill, Les Chefs de France, Yachtsman Steakhouse, and Ohana.
-Look into some non-park things to do. Fort Wilderness has lots of options. We went on a carriage ride on our honeymoon, and we loved it. I understand that they have horseback riding, bike rentals, etc. Anything that gets you away from the crowds for a bit helps your trip feel more romantic.
-I would consider some of the tours. We did a few special events at Food & Wine Festival and had a fantastic time. I think the off-the-beaten-path stuff makes you feel like you're getting more out of the World.