The differences are:
Back of ship: Magic has Goofy, Wonder has Donald and his nephews
Dining room: The most formal of the rotation resturants is Lumieres on the Magic; Triton's on the Wonder
Atrium statue: Mariner Mickey on the Magic; Ariel on the Wonder
Entertainment District: Beat Street on the Magic; Route 66 on the Wonder
I also believe that the Magic is Art Deco styling while the Wonder is Art Nouve.
These are all really minor changes and the rooms, entertainment, etc. are all the same. Can't go wrong with either one!