I had the same issue picking a version, but I went with the Xbox 360. Here are the main differences that I saw:
Xbox 360: HD graphics (although simple visuals, I play on an HDTV) Achievements (always fun to add to the gameplay) Wired Portal of Power (no batteries - a plus for me)
Wii: Motion control (easier to control, best for some kids) Wireless Portal of Power (convenient but uses batteries)
What really sealed the deal was the price. Maybe if the Wii version were $10 cheaper than the Xbox 360/PS3 versions (which is usually the case), I would have gotten the Wii version instead. But for the same price and playing in HD, I went with Xbox 360. I don't need motion controls in a game, and I'm not going to be moving the Portal of Power around a lot, so having it be wireless wasn't much a bonus for me.