Ok, the story for the boss battle right now is uncertain (I'm going with a GLaDOS teamed up with Bowser to make a Mario bot thing) but here's my idea.
The single-player battle starts out with Robo-Mario on one side of the room and you on another.
Firstly, Robo-Mario will start to fire his portal gun which spawns Bullet Bills. (It only shoots one portal, go figure.) He stands without moving at this point, touching him shrinks or kills you. You have to redirect the Bullet BIlls back at him.
Once he is hit by one, his portal and the Bullet Bills desintegrate and the walls begin to crumble. He shoots tons of portals all around and moves, all of them spawning enemies (spinies, goombas, bullet bills, ...LAKITUS...) His eyes will turn green (that's your cue) and you must stomp him or maybe kick turtle shells at him a certain number of times (3 maybe.)
Once that happened, he starts back up again in his first form, but the room shifts into different and more challenging positions each time. An example:
After shifting through his phases a good 5 times, he explodes into flames. (yay)
With two-players, one will have the portal gun, and one won't. The first player will be in a small box made of Light Bridges (one with the p. gun) and the other will be outside (the one without.) They will have to work together to be able to beat him.
With more than 2 players, maybe the balance can be offset (1 person with portal, 2 people without, etc.)
If the 2p can't be done, at least the battle isn't broken with more players.