Japan is being built already because, A.) they are trying to finish by the 2020 Olympics, and B.) they REALLY don't have much extra space around there to go further.
Anyway, if this idea of them making another gate for Nintendo is true, I think it makes sense, in the same way that MGM Studios worked for Disney as another park destination, instead of the original plan to just add an existing ride to EPCOT.
They have the property now, so they can add more days to passes, give people one less day to go to Disney, expand much farther than the somewhat cramped space they were planning to go into with 3 lands, and we knew that Zelda and (longshot of Pokemon) being part of a park were options.