Nintendo hardware may not be benefitting from all of the main-series Final Fantasy releases, but the recent arrival of Cloud in Super Smash Bros. and the upcoming release of Final Fantasy Explorers in the West are both indications of the solid relationship between Nintendo and Square Enix.
Another small piece of evidence in that case is today's arrival (22nd December) of Final Fantasy VI Advance on the Wii U eShop in Japan. This Game Boy Advance port arrived in 2006 and added some additional content to the classic RPG; the SNES original did previously arrive on the Wii Virtual Console in the West as Final Fantasy III, so it'll be interesting to see whether this GBA version will also make its way to Western Wii U systems. As the GBA port in question did have a global release at the time it certainly seems possible.
You can see a trailer for the Japanese release below; would you be interested in picking this up on Wii U?