Also it's been rumored that Microsoft has a contract clause stating any multi-platform games that have a 360 release planned must be delayed to release with the 360 version.
Flip Flop of God: Over how much of the game the Murphy sections took up. Part of it stemmed from some of the Ubisoft staff's limited knowledge of English.
So is it a Wii U exclusive or not? First they said yes, then no, then yes again, and now they're saying no once more. It ended up as a multiplatform title (Wii U, X-Box 360, Playstation 3, Vita and PC) with the release delayed until September 2013.
Refitted For Sequel: The first game was planning on using a world based upon different art styles, but was scrapped early on. This game's premise is the protagonists getting trapped in a painting.
What Could Have Been: The NFC functionality, as it has been confirmed that no launch/launch window Wii U title (including Skylanders: Giants) will use it. Although time will tell if it will be patched in the future thanks to Nintendo announcing their own line of NFC figurines called "Amiibo."
The game was also meant to be exclusive to the Wii U console at first with a launch date of February 2013. The poor sales of the Wii U exclusive ZombiU prompted UbiSoft to make it multiplatform instead, and delayed the release of the Wii U version to coincide with the release of all other versions of the game. Wii U owners who felt this was a missed opportunity for UbiSoft to at least make the game a limited time exclusive during a "drought period" in the Wii U's early 2013 release schedule (some developers on the team even said the game was basically done at the time of the delay) did not take the news well.