Nintendo hasn't even created an offshoot of the game for it's own IPs yet. Know who has? Disney. Nintendo continues to leave money on table while at the same time releasing a console like the Wii U.
They have already; Pokemon Rumble U.
It's similar to Skylanders in that you can get additional characters by purchasing physical toys, however unlike Skylanders, all these guys are available in game. The physical toys just keep the powers/you can upgrade them and what not. B/W Kyurem are also super strong.
I don't think the game was well received, so I'd say its probably unlikely we'll see another any time soon unless they make it huge game. If you're referring to something where there's all Nintendo characters appearing, that's kind of the basis for Smash Bros, but if they made a NFC Smash Bros game, you can bet that literally everyone would have a bitchfit about it.
They're not leaving money on the table so much as they've already tried it and seemed to have bowed out.
And we can't forget that for all intents and purposes, Nintendo WAS going to have a lot of NFC stuff for the Wii U; that's the whole reason it has the NFC reader on the Gamepad. We saw Rayman Legends using it a lot in the E3 trailers stuff.
Once it was revealed that the game wasn't going to use it (and that Rayman was getting delayed) it probably killed off most of the internal hype on using NFC for games.