The only thing that could reverse things is if the Vita cold run a 3DS emulator. And even so it would be weird with 2 screens beeing risized in one.
With that said, i like the direction the Vita might be taking in the future. Indies + Japanese games beeing brought over + some good first party exclusives every year. That makes the system worth it.
I do think Nintendo is gonna make the Wii U a very important focus in the next 2 years. But some of their teams always work on 3DS games. I would be surprised if we didnt get another pokemon game by gamefreak 1 to 2 years after XY.