Pikmin would make an excellent Pixar style animation, hints of Wall E and Bugs Life, although Universal wouldn't be the best fit IMO (at least based on Universal Animation Studio's past output)

Super Mario Bros, done right this time!

Also, don't mind if these movies would be CG or classic animation, as long it's no Live-action

metroid

space exploration and blowing up aliens would be awesome.

Metroid and Zelda.
Fire Emblem should be more like a Game of Thrones clone.

Metroid and Zelda should be live action, while all the rest can be pure CGI. Honestly, they could take a page out of Marvel's book and make individual films for the core franchises (Mario, Zelda, Starfox, Metroid, and Pokemon), and then have it all come together in an Avengers like film with Super Smash Bros. Master Hand could be the central antagonist of it all, and they could delve deep into what exactly he is and why he brought the Nintendo universes together. It all could take a while, but if they had multiple projects going at once, it could work.

We NEEEEED a Zelda movie
As for Xenoblade, I would much rather have a anime of it, as the story is way to long to fit into an average 1 and a half - 2 hour movie