I've been to both and we are going to the FQ this October.
We were at the FQ 11 years ago on our honeymoon and to Riverside last year (because FQ was closed). FQ is very quaint. When we were there 11 years ago, they had a sit down restuarant, but from what I've read, it is no longer there. If we were to do sit down, it would be in DT Disney or in EPCOT, so we wouldn't need sit down at the hotel. The size of FQ is very easy to get around and it also has a boat launch to DT Disney.
The Riverside is very nice as well. We stayed in the mansion rooms, right next to one of the quiet pools. It was the closest building to the bayou (not sure of the name) so it was easy access to the main building. It does have 4 bus stops, but we always went to the main one, so getting on wasn't an issue. I do know that when we were at FQ the bus would stop by us first and then go to Riverside. Many times, the Riverside guests had to stand or weren't even let on at all. This may have changed in the last 11 years. You could always walk to the FQ. It is a pretty walk along the river.
As for which one to stay at: DW likes FQ for it's landscaping, pool, one bus stop and overall feel. I would lean towards Riverside for the pool for our son. Rooms are equal, but more spread out. Draw back of Riverside - twice as many rooms = twice as many people. If it's your honeymoon, you may want to go to the smaller hotel. You won't go wrong with either resort.
Have fun and congrats.