why not have it similar to mario 64 ds where, when you save the main characters, you could play as them and they could do things you couldnt. you could also bring stories and characters from the other mario series like wario land and the star children from yoshi's island and so on
...and Waluigi. Don't forget Waluigi. The guy needs to appear in a mainstream game.
The only things characters did differently in SM64DS was the special blocks that gave you abilities, and every now and then you would NEED a character, like Mario for the race missions with that Koopa guy whose name escapes me, and for the Bowser battles. They would really need to expand on the different moves and attributes. Maybe Wario could use his shoulder bash move to break certain walls and blocks, and we all know Luigi can jump higher then Mario, giving him access to new areas. Waluigi could run up walls or swim through the air for a brief second. Mario has the basic moves.
As for power ups, they could bring back the switch blocks that you had to find to activate the colored blocks. They all get power ups like the fire flower, mega mushroom, and tanooki leaf, but everyone has their own power ups. Mario gets the wing cap and p-balloon. Luigi could have the invisibility cap and boomerang plant. Wario would have the metal cap and the power garlic, which allows him to do a long shoulder bash charge breaking even bigger blocks and destroying larger enemies. Waluigi mini mushroom and tornado flower, which gives him the ability to spin upwards like the propeller suit did, just it looks cooler.
Man, I need to stop writing so much...
