As an easter egg, Samus being in F-Zero would be cool I do admit... but I wouldn't try and write her into any story if it were me, I'd just have her in there for the sake of it being an easter egg.
I think I'd like to see new IP's set within different franchises worlds. I can't remember who it was that posted some suggestions years ago but they made the suggestions of an MMORPG set in the land of Hyrule whereupon you'd choose a race (Hylian, Goron, Zora etc) and that would determine how you played the game etc.
Another suggestion was in the Metroid universe, where you'd be a member of the Galactic Federation Forces set on SR-388... I think they said an FPS which intrigued me at the time.
In this they were saying how you could be playing and all of a sudden you'd see a huge fight going on between Samus and a boss character in the background and you may have to assist somehow.
I liked that idea.