Well, a portal gun is a pretty weird tool, since it doesn't really fit the challenges that SMB give you. (Why would you portal a goomba into a pit when you can just stomp him?)
So the level design would at least be different to take advantage of the portal gun. Most of the portalable areas in mari0 are just the ground, and that's really boring. So I bet that hypothetical Super Portal Bros. game would use a bit more the second dimension. (Having more ceilings and walls, like in the castle levels, or test chambers)
To teach the player how portals work, the level design could copy Portal's first chambers.(IE auto-placing the portals at first, then give the portal gun to the player.)
The portal gun is not a tool you can use as quickly as the jump or fire buttons, since you also have to aim. It's intended for puzzles, not for action games. But unfortunately, if in Super Portal Bros. you just have the portal gun and nothing else from Portal, the range of puzzles you can make is quite limited. You can basically do this with just a portal gun:
- Access platforms that are far enough that you can't simply jump on them but close enough that they are not offscreen.
- Do a portal loop to get propulsed over a large pit.
- Kill or portal enemies out of the way.
That's all I can think of. So to make a good game, you need to have "test chambers", to focus on puzzles, and for that you need to add other puzzle elements. And at this point you have pretty much a 2d Portal.