Mega Man would find the correct order to destroy them in one by one.
I'm guessing Mario first, giving him the Fire Ball power. Fire Ball works good against Link, which gives him the Boomerang power. Boomerang disables Belmont's Whip giving him the Whip power. Bowser is a huge masochist, given his roles in the RPG games, so he'd probably enjoy the whipping, giving Mega Man the Shell Bash power.
Then Samus descents in her space ship, like Wiley. A series of battles takes place, first Samus in the ship, then Samus in her suit, Samus out of her suit...
Yup, Mega Man has got this covered.