The ships are almost identical. They have the same deck plans, but there are differences in the decor and the theming of some public areas. The are essentiall the same, though.
The big differences are that the Magic is done overall in an arc-deco style, while the Wonder is art-nouveau. Two of the restaurants are the same, while the midship restaraunt is different. On the Magic, it's called Lumière's, with a sort of Beauty and the Beast theme; on the Wonder, it's called Triton's and is has a nautical/Little Mermaid theme. The buffet restaurants are different, with "Beach Blanket Buffet" on the Wonder and "Topsider's" on the Magic. There's not much difference in them, though. The night clubs on deck 3 are different, too. The Magic has Rockin' Bar D as the main club, the Wonder's counterpart is called Wavebands. The small club is called Sessions on the Magic, and is a Piano bar, while the Wonder's version is called Cadillac Lounge. The third bar on the Magic is called Diversions, and is a kind of neighborhood pub/sports bar. On the Wonder, this is called Barrel of Laughs and I think still hosts a dueling pianos show. This will be changed to a Diversions-type club (not sure yet if it will actually be called "Diversions") when the Wonder goes into drydock this fall. The only other differences are with the teen club. On the Wonder, the teen club is on deck 9 and the sports bar, ESPN Sky box, is in the forward funnel. This was changed during the Magic's last drydock and will be changed on the Wonder this year, too. The teen club is now called "The Stack" and is in the funnel on the Magic where ESPN Sky Box used to be, and what was the teen club is now an adult coffee bar.
Palo, the adults-only alternative restaurant, is the same on both ships, as are the Walt Disney Theatre, and the staterooms themselves.