As others mentioned, not owned by Nintendo, but also Rare was sort of spent as a creative force by the time they were purchased in 2002.

They lost a lot of developers to Free Radical.

I'm not sure what Microsoft acquired with Rare because besides Viva Pinata and Sea of Thieves the company has basically produced junk over the last eighteen years. They're not even in control of their main IP: Perfect Dark as Microsoft has parcelled that out to another studio for the reboot.