Well, it sure isn't going be to smash attacks because that wouldn't make much sense and they would have to be done in a way where Shantae isn't going to be wide open to attack. Maybe it's addressed in the first page but I only see Shantae being more like her Pirate's Curse self but with her other genie stuff. Maybe I prefer it that way too since it will make Risky a likely echo as well.
Inkling also has different weapons as Smash Attacks.
Plus they quickly switch back and forth between human and squid forms in some of their attacks.
So I don't see rapid formshifting for single attacks being an issue.
It isn't for Inkling and it shouldn't be for Shantae either.
Another solution, like I suggested. Is make transformations seperate playable entities, but with much smaller movesets.
Like only two or three attacks, serving the role they excel in.
Either option works fine for me.