I want to see a Toad say "Thank you, but your princess is in another castle."
Then a short pause, then:
"And you're not really Mario."
Then Snake wakes up in a cold sweat, in a tent. He zips it open, just in time to realize that not only is he on an alien planet with 3 moons and 2 suns, but giant Giga Bowser is right there, breathing fire, roasting Princess Peach alive. Snake screams "Nooooooooooo!!!!" Credits. Then after the credits you get a bonus 10 minute cut scene of Mario discussing the politics of being a vigilante plumber after the fall of the Mushroom Kingdom, and how this time, it's personal. Then you get a secret code to enter at the web site to unlock a secret trailer for the sequel. The sequel can be either the OP or forest-spirit's idea. They don't need to explain why Peach is alive again either. They can just have a giant gaping plot hole and call it art.