I don't think it will on Wii U
From the Animal Crossing producer just this past March:
http://www.polygon.com/2014/3/28/5555682/animal-crossing-interview-new-console-version-smartphones
"The current gameplay style of Animal Crossing is best suited for a portable device," Eguchi said, "but if we were to create an Animal Crossing for a home console, I think we would really have to invent a new style that's suitable for the platform. The environment in which the player is playing the game is very important, so we need to think that through before we start creating something like that.
"We might not have been able to do that for Wii," he said, "but whether it's the Wii U or a future hardware, it's important to think about what environment the player will be in."
I think it's kinda of eye brow raising that he mentions a "future hardware" platform. Also it seems that even up to March of this year they're still not sure about a Wii U version, assuming development takes about 2 years+, that's not exactly a good thing. If there was an AC for Wii U IMO it would be well into development right now the above quotes sound like they're not even sure if they want to make one on the Wii U.
IMO if will be a launch title for the HDS/Fusion (whatever you want to call it). That *must* have a strong launch or Nintendo is screwed. In the long run it would also probably sell better than a Wii U version, making it an easy call for Nintendo.