I think it's matter of a building number request when it comes to Alligator Bayou. We used to stay there all the time because we needed the trundle beds and I would always request buildings that were further into the resort away from the parking lots. That way there was no chance of me looking at a parking lot, or hearing the busses. For instance buildings 18, 27, 26 on one side and 38, 39 on the other. These buildings are more on the inner ring of the Bayou. We always got our request. Perhaps we were just lucky.
While we never stayed in Magnolia Bend so I can't really compare - we always loved the Bayou. I never thought it was dark or a downer. We always loved the rustic feeling in the rooms. We also loved the grounds. They're extremely tranquil. It's very natural as opposed to the Bend which is a little more formal looking. Curvy natural lines as opposed to straight planned lines. (Although I guess it's all planned but you know what I mean!) We always loved the kids running around the Bayou grounds chasing lizards and walking over the small bridges. It's a beautiful place. Plus, I love the free form shape of the quiet pools as opposed to the rectangles of the Bend pools. Both beautiful areas of a beautiful resort just a different feeling in each. We haven't been back in years because we just can't fit now that the three kids are teenagers, so we've been slumming it over at The Yacht Club. But if I were to go back, I would immediately book an Alligator Bayou room. I miss it.