Metal Gear Solid 3D: Snake Eater also came out a couple of years after Snake in Smash, but Nintendo had already collaborated with Kojima by that time on MGS: Twin Snakes which Nintendo had their own 2nd party work on (Silicon Knights).
Speaking of which I think you'll see a lot more Konami content on Switch. They're probably pretty happy with those Bomberman R sales.
EDIT: If you actually go back to the 3DS unveiling E3, the "Metal Gear Solid franchise" (not just MGS3) was supposed to be on 3DS. I'm guessing the PSP MGS series was meant to continue on 3DS perhaps, but Konami didn't like Snake Eater 3D's sales and/or became enamored with mobile. But at the time it even got the loudest applause from the E3 crowd:
https://youtu.be/Fa5mPHFOg8A?t=2m
