While One Piece certainly has villains like that, not every story arc is like that. For example, the recent arc was just a big war between two forces (three? four?), and Luffy and co also do questionable things just for the hell of it like storming a Marine fortress. You have to remember that in the world of One Piece, the main cast *are* considered the bad guys.
So no, it's not typical shounen formula.