Nah, you build the levels just as you would, and focus on the characters as secondary things. Some of Super Mario World didn't work properly with Luigi when it was re-released on the GBA. Sections where you had to run a certain speed to make it through, and tall Luigi couldn't make it fast enough, so he'd take a hit or die, or whatever would happen.
They can make the game around Mario, then just do whatever they like with the characters. The issue with the Subspace Emissary isn't the same. The focus was on combat, and not level design, at all, and as such, it left much to be desired. In addition, most, if not all characters were modified so that movement speeds and jump heights were very similar when it came to the Supspace Emmisary.