They're still worlds apart. They deal with completely different themes, lores, and concepts. They're built as very different universes.
If I absolutely had to pick the best mesh with Metroid, it would be as others have said: F-Zero. Simply because there's no really significant thematic inconsistencies between the two. Both are science fiction. Both exist in human filled universes with a strong alien presence. Both take themselves relatively seriously. Both, in art design, are more closely interchangeable than anything else.
Yeah. Stuff like Kingdom Hearts, and Smash Bros, exist in a "what if?" universe where the aim is to merge everything together, recklessly even, just to see what happens. A Nintendo All-Stars RPG style thing would work fine with this too, as the ideas is "ITS EVERYBODY! TOGETHER!", and therefore becomes it's own contained universe in a sense.
I'm going to throw an idea out there that will sound crazy.
What if...Retro plans to completely reboot Star Fox...not just by throwing Star Fox in a new game...but they plan to change a lot of things that we know about the franchise?
Obviously a lot of people feel like Star Fox has gotten lame or ran its course.
What if Retro is not just planning this game to be a Metroid x Star Fox game...but a chance to take Star Fox in a completely different direction? I'm talking mood and atmosphere in a Star Fox game that is dark and moody along the lines of Metroid.
There's this belief that Retro will just take the Star Fox we all know, and will just throw it into Metroid. I don't believe that. If anything, I could see Star Fox going through a transformation to make the franchise more appealing to today's gamers. Possibly taking Star Fox into a more darker, and less cheesy direction. Which would make it fit within Metroid's world better.
Again, I think Nintendo plans to completely reboot Star Fox from the ground up.