In my opinion, the transformation aspect of Shantae is its weakest element- while it is supposed to help with dungeon and overworld traversal, the dance mechanic is cumbersome, tedious, and few of the transformations are actually fun to play with.
Pirate's Curse is the one game that I would say has the fewest flaws, with the only real one being its unnecessary stealth segment. GBC is the epitome of a handheld game of its era trying too hard, and Risky's Revenge is convoluted, short, and not very fun.
That being said, I think that if Wayforward has the time and money to do what they want, they come up with great products. That's why I backed Half-Genie Hero despite its departure from the series' formula.