While I do feel that, in some places, the comic relief of Pirate's Curse may have been a little overdone as well as the game having a few cheesy moments, I don't get what this guy's talking about. About the only difference in Shantae's personality between it and Risky's Revenge is that she was drawn with multiple expressions rather than the two drawings she had for dialogue in RR, and there being more dialogue in general. I will say that I didn't care for Pirate's Curse being a whole game about Shantae losing her magic (minus her hair if that counts, they've been vague over whether that's magic or not), but I understood what the writers were trying to do with it in terms of tying the events of RR, PC, and Half-Genie Hero together.
For the record, the Squid Baron now seems like less of an enemy and more of a self-aware video game boss. Though even before that, he was there to actually help Shantae in the last few events of Risky's Revenge.
The Metroid Prime trilogy should still be canon. To my knowledge, the only thing that happened is that Sakamoto said on one occasion that they merely weren't "his vision" of the games. I don't think he ever said "yeah, this never happened".