The chief creative officer of Sega, Toshihiro Nagoshi, was recently interviewed by Edge magazine about his career at Sega and creating games like Super Monkey Ball and F-Zero GX. At one point, Nagoshi mentions that before developing F-Zero GX, Sega had made a few proposals for games using Nintendo IP. One of these was Metroid! Apparently, the proposal was rejected or went nowhere. Nagoshi added that he was more confident in making a driving game, hence F-Zero GX:
I really liked the Super Famicom game [F-Zero], and while we made a few proposals – Metroid for instance, and others – I was most confident in making a driving game because of my experience in the genre, though I’d never make a sci-fi one.
There you have it folks. We could’ve had a Metroid game developed by Sega. Maybe in the future they’ll get their chance.