Everything you're saying about the craft of the show is right, but there's no reason why a character can't be a protagonist who also contains forces of antagonism. Indeed, the show's thesis is that we as human beings are messy, complicated, self-serving creatures who are the Perfect Unblemished Lead in our own life story, even if we are the villain in someone else's - and particularly if our casting them as the villain is actually what makes us the villain in the first place. So the critique about how many story lines are present (but centered around Mary Jane, who is something of an Alanis/Diablo/Paulus figure) is simply to not like what it's doing, rather than a condemnation of its craft. Its craft is solid, you just might not care for the taste.
Meanwhile, everything the OP says is also true about the show. These different viewpoints aren't in opposition; they are the very the fabric of the play itself. The show is big enough to hold all of those contradiction, and this is what makes it most radical as a piece of Broadway entertainment (or maybe not - many of the great musicals of the Golden Age and today are complete messes in terms of story structure, and yet they prevail).