I think the best way to handle her transformations would be making them directional specials and having each special have its own follow up.
Shantae's transformations kinda only serve one or two purposes and it feels like a whole transformation would be limited and while it seems cool in theory, to me it feels like it would be a little clunky and not feel great in practice.
There's a difference between Pokemon, who have whole move pools to pick from, and something like Monkey Form, which has a high jump, the ability to climb walls, and the monkey bullet. Shulk's monado does have different modes, but they only enhance his base stats, they don't give him moves. I just don't think Shantae's transformations would work well when used like the Monado or Pokemon Trainer.
But who knows, Sakurai is a wizard, he could make something fun and interesting with them for sure.