But yea, as I said, I agree: it perfectly fits the motif of the game that JBJ is the last boss. This game over the first is way more about the consequences of your actions, something we're both told at the first and last fights. You can't just go around killing without reparations; or at least, regardless of who it is, when someone dies... people get hurt. Travis even begins to learn about the sanctity of life toward the end, that people are human regardless of how fucked up they are. And taking lives like this is senseless... even no name nobodies that Travis's kills in the first game end up having repercussions that cost him greatly. After Margaraet this transformation in him is complete and he vows to end the UAA. Which I imagine, he ultimately does, since after an undisclosed amount of time Sylvia is working a stripper booth in another town, obviously a bit destitute.
That's another thing I really enjoyed about NMH2... the characters actually demonstrate notable growth over the course of the two games. In the 2nd one, Travis has obviously grown up a bit. It's less than a game for him, he doesn't go around 'fucking by killing' his enemies. He takes this more seriously, he's passionate and not bored. He actually begins to care about who he's fighting, he understands at the end that he's not stuck in some game as much as caught in an emotional cycle of dependency that's being exploited and needs to end. The Margret fight really is a big turnaround for him. And he comes to terms with his feelings for Sylvia in that they aren't just lustful, he's sees her as also trapped, a kindred spirit. Sylvia as well, you can subtle tell, she cares deeply for Travis in this title. She mourns his loss throughout all the phone conversations and yearns to hear his voice. She kills Ryuji not because of her job, but because she doesn't want him getting stronger to come back and kill Travis. She's being overtly defensive and it's her way of protecting him. She obviously calls in Shinobu since she feels Travis is getting worn out and needs rest and displays signs of jealousy around her. And at the end, she's very world weary and ready to rest. Shinobu is an interesting case, she left a high school student to prove herself and comes back at the age of 21 and in a confused state... rightfully she had a screwed up childhood so she doesn't entirely know how to deal with her feelings for Travis, she throws herself at him like she's still a teenager as she finally starts 'catching up with the curve' so to speak emotionally. Henry had very little screen time, but you can see even he doesn't care about petty vengeance anymore. He's not burnt by his divorce with Sylvia, he comes to help his brother, and goes on his way (without losing his playfulness).