It reads like fan fiction and the rumor's original reporter—who uncovered PlayStation All-Stars six months before it was announced—concedes that nothing about it is confirmed. But Retro Studios is said to be working on, or at least to have considered, Star Fox-Metroid Fusion Saga, a mashup of third-person action gameplay with aerial/space combat.
Paul Gale Network revealed the first images of Sony's Smash Bros.-esque fighting game back in November, which has since been confirmed along the lines it was originally described. But in that story, the publication had a mobile phone picture of a screen at the time. Paul Gale Network concedes it has no secondary proof of this concept and admits this may have been discarded long ago, back when Retro was pitching ideas and Nintendo was looking to send the studio a new project.
Kotaku reached out to a Nintendo of America representative this morning and was told that the company, per longstanding policy, does not comment on rumor or speculation.
The concept involves controlling both characters in their familiar gameplay environments, with moments of switched roles; Samus' ship would be pilotable like Fox McCloud's; McCloud would be a character in a third-person sequence. A very detailed description is at the link. If it's on the level or bogus, I suppose we'll find out at E3 in a couple of weeks.
RUMOR: Is Retro Studios' Wii U game "Star Fox – Metroid: Fusion Saga"? [Paul Gale Network]