You are saying it wouldn't work, and i'm trying to figure out how that would be. Mind stating why you think it wouldn't work?
Because they're thematically different franchise. Simply being science fiction with animal aliens isn't enough. Both Star Fox and Metroid have established lore and history grounded in different themes.
Star Fox is a tongue-in-cheek Thunderbirds-like alternate reality with anthropomorphic heroes and villains based on real world animal species: dogs, wolves, falcons, pigs, and so on. Star Fox can be surprisingly grim and serious at times, but the universe itself has always been a cheesy anthropomorphic reality. It has been consistent in this as well. Star Fox Adventures plays in the idea by introducing a planet full of talking dinosaurs.
On the other hand, Metroid has always taken itself a bit more serious. In art, themes and lore, Metroid attempts to create a more realistic 'science fiction' universe not unlike Alien (which was influential in designing the first Metroid). Yes, there's bird people, but they're simply an avian based space faring species. Space pirates are just aliens, nothing more. Every other creature you meet in the series is a uniquely developed life form used to convey the evolutionary lifeforms that inhabit particular planets. On top of this, Metroid has crafted a specific, human based lore and universe, something Star Fox has not.
Lastly, both series utilise different art directions. Star Fox has always had a more comical, puppet like like to proportions and designs, meanwhile Metroid has kept itself grounded, with realistic proportions to architecture, armour, weapons and creature design.
They're no more or less incompatible than the examples I mentioned, but the point is that combining them is completely unnecessary and problematic when staying true to the franchise' origins. It requires changes be made to either one series or both, on a thematical and artistic level, to combine them in a way that wouldn't come across as a gimmicky Smash Bros.-esque crossover.
In terms of the design, there's nothing written there that couldn't work wonderfully as a stand alone Star Fox game, or a stand alone Metroid game. Combining the two will do little more than alienate majority of the fanbases for
both franchise, while creating a weird hybrid that I cannot see appealing to anyone other than a niche audience. If Nintendo did this, it would be clear their interest is not in growing either franchise, but killing them and rebooting them for a new generation.
And that I'm not interested in.