He wasn't intentionally the final boss though. He wanted to be left alone, then softened and had a little community going. The crusaders purged his community but couldn't kill him, so he retaliated to make them understand what they'd done (and they even repented). But that in turn perpetuated the cycle of violence he didn't start.

He chose to break the stalemate by leaving under the guise of being killed by the strongest crusaders.

Then, the cycle repeated when he found himself in Tokyo. The difference so far is that he reversed the cycle before it could get going, and the group who unknowingly attacked him is willing to let things play out while he gets his bearings.

As for Misaki, sure, she encountered a tragedy and turned vicious, but I thought it was interesting that she wanted to try murdering an innocent to see if she had fully turned into a monster or not. She killed the original Polka, and then her very next step was to kill herself. Like, within minutes of completing her first true murder. I'm guessing she didn't like how killing an innocent made her feel. That's a lot more interesting than Murder Frenzy Bishoujo that we usually get (including in DRRR).