I initially explored AndEngine because it seemed to be the more popular choice of the two. After spending some time with AndEngine though, I felt apprehensive about how much it abstracted from the developer. For some, this is a good thing because it means there's less you have to worry about and less starting friction. Personally though, I prefer my frameworks to be more bare bones.
This prompted me to Google search "Libgdx vs AndEngine" and found the following analysis by the developer of Libgdx very helpful. After a little more research, I finally decided to go with Libgdx, and the following are the selling points of Libgdx that won me over
- Code once and compile for Android, and HTML5
- Lighter weight than AndEngine
- Better documentation