Wouls you prefer a Xenogears remake, a Super Mario RPG 2, or the Final Fantasy VII remake.
I obviously choose the Xenogears remake. It could signify two games in seperate Xeno series making their way one home console, and with two companies sharing the bills and profit, Takahashi may be able to realize his full vision of that game, and sequels. Hell, they could also bring Xenosaga HD to the switch (which is known to be a magical funding fairy away from happening) and you could experience the whole Xenoverse on the switch.
This would mean Takahashi may have to take a step back as director, and become more of the overseer of the Xenoverse, but he and Soraya Saga could easily just come up with character designs, story, and as I said, oversee the projects. It could mean a start to the Xeno empire.
But what about you?
(Edit) I have only used these options because I wanted to keep this discussion focused. There are a million things I could have put, but wouldn't really require a Nintendo partnership (Crystal Chronicles, Bravely), or just didn't seem financially sound (a partnership with Nintendo for a FF VI remake). The options here are simply games that need a collaboration (Xenogears, SMRPG2) or are already in development and may need a little bit of wheel greasing to come out on NS (FF VII Remake). These simply are the 3 easiest options I could see coming from Nintendo and SE.