We have stayed in both. I love the look and atmosphere of the Alligator Bayou a little better than the Magnolia Bend. The paths from the main building to the Alligator Bayou are lined with lots of plants and flowers that make you feel like you are in a tropical location. I also think it was much more convenient for the buses. It seemed like we always had no more than a 5 min wait when we used the stops by the Alligator Bayou. It also seemed a little more private. I also think the inside was cute and I loved the wood look in the shower area. The lack of drawer space wasn't really an issue for me because I used the hanging rack in the sink area, that that is something you may want to take into consideration if you have a lot of clothing and need more storage space. One thing that may be a little annoying for some people is that if you are in a back building in Alligator Bayou, the walk to the main building can be a little long and the paths can be confusing if you aren't paying attention. Magnolia Bend is lovely in it's own way. It seems a little more grand when you are walking up to your building and for some reason a little shorter of a walk to the main building even if you are in a building a little farther away.
I would personally choose Alligator Bayou (even when not traveling with our girls).