Before Project M, I had a vision of Zelda as a situational tool for Sheik. Zelda, in her princess form, should naturally avoid fighting, right? Obviously we're not going down that road. The instant-transform is neat, but I imagine it would only feel useful if Zelda and Sheik synergized in some concrete way. With that said, designing one character around the other would be too cumbersome. I don't really have a preference one way or another on whether or not Zelda and Sheik are separated.
However, I do think something like instrant-transform would do wonders for Olimar's Pikmin order. So, Olimar would pluck Pikmin of one colour and change all of his Pikmin's colour by whistling.
This would be the order: Red > Yellow > Blue > Purple > White (just like in the games)
Whistling with down+b changes colours right by one on the cycle, whistling with down taunt changes colours right by two on the cycle, whistling with side taunt changes colours right by three on the cycle, and whistling with up taunt changes colours right by four on the cycle. So, Olimar would have no taunts, but keep in mind that playing as Olimar is pretty disrespectful to begin with.
Also, Olimar's whistle would do small (1% at really close distance) aoe damage. This way Olimar could attack with one Pikmin colour, extend a combo with a carefully placed whistle, and continue the combo with another coloured Pikmin.