I would also pick Wilderness Lodge. However, unlike others in this chain have reported, it's been loaded with kids when we've been there (in offpeak!) -- running in the lobby, yelling in the mis-named "Whispering" Canyon Cafe, etc. I think it attracts many young families because the boat transportation to MK is very convenient, yet the hotel costs less than the monorail resorts.
Having said that, it is a beautiful hotel and Artist Point is a lovely, though often noisy, restaurant. If you want quiet, eat after 8:30 p.m. Perhaps the nicest thing here would be to do concierge, since it is your Honeymoon. My sister and her family stayed WL concierge recently and said it was truly lovely. The CMs were very helpful and wonderful, the food offerings were great and it was somewhat removed from the hustle and bustle. Moreover, even though many complain about the closed balconies on the concierge floor, my sister didn't mind it at all. And for a honeymoon they might be perfect -- more privacy. And, concierge at WL is the least expensive on property and, I understand from these boards, can sometimes be obtained for $50 or so per night on checkin.
One last suggestion -- don't forget about AKL. We stayed there concierge recently and it's our favorite (we've also stayed WL, Poly and Boardwalk Inn). It often has very good discounts available. The resort is beautiful, and it seems much quieter than other places we've stayed. The CM's are great, the restaurants are great, especially Jiko, and we thought the bus transportation was fine. The trip is longer, but the buses serve only AKL, so no stops on the way. I don't think the bus to MK takes any longer, really, than the boat from WL by the time the boat stops at the Contemporary Resort and Ft. Wilderness Campground. And, the animals are endlessly fascinating. AKL, perhaps more than any other Disney resort, truly transports one to someplace that is unique, exotic and far away -- just what one wants for a honeymoon. And the Sunrise Safari for concierge guests is not to be missed.
One more suggestion -- pick up a copy of "Walt Disney World for Couples" by Rick and Gayle Perlmutter. The latest edition is just out. It has great ideas for making your WDW visit truly romantic.
Whatever you choose, have a wonderful honeymoon!