As has been said previously, talks between Nintendo and Electronic Arts were not successful, and the two companies were not able to work out a deal. Since Crytek had no publishing license for Crysis 3 on the Wii U, they had no options. Crytek could not release it with the studio itself being the publisher, so the Wii U version of Crysis 3 died.
It seems that there is always more to these stories than meets the eye.
You can read more here at Venture Beat.