Yeah. First time thinking of SE boss ideas. Whatever.
The room would be a completely closed off square of unportalable blocks, with a slightly thicker right wall.
Phase 1: Shadow Mario is sitting in a stand in the top right of the room. Pretty much unreachable. At least until he starts firing homing rockets that can hit a tube flowing Blue Gel. The blue gel covers a part of the floor, and you would use it to jump onto him. 3 hits would take him out. After the 1st hit the rockets get slightly faster, not fast enough to be outrunnable but fast enough to be (just barely) noticeable. He then repairs the tube with some funky button on the stand and this also leaks water into the room cleaning the gel. After the 2nd hit he repairs the tube yet again, cleans the gel and drops 2 bombs in the room, the rockets don't get faster. 3rd hit, his stand explodes as he falls to the ground. But wait, there's more for this special offer...
Phase 2: Shadow Mario takes out a controller, hits a button and gives himself 5 mushrooms, increasing his size to pretty much stomp Bowser's sizes into dust. The right wall breaks, and you are forced to escape the hard way. Shadow Mario is constantly chasing you to the right, through some unused test chambers. One test chamber has a portal on the wall infront of you, while the other, behind a solid wall and unreachable switches between the way to go and a free ticket to death. Rest of the idea is up to you guys, because I'm lazy.