The villain definitely seemed petty and self-centered at first, until her real motivations were delved in to. Then it got kind of dark and sad. And as for Touma, it's been mentioned a few times now that not only is that a core aspect of him, but how people view him is somewhat distorted, viewing him as a righteous hero when really all he's doing is whatever he feels like. And while people are still going to view him like that, it was definitely nice to see character development on his part throughout New Testament. From worrying about how his actions might be used for other's personal gain, to deciding that sometimes he needs to do things for his own personal benefit as well.
Really, though, the whole thing with Misaki is kind of depressing. When he mentioned remembering her scent, it made me think that maybe this isn't the first time she's popped up to him since he lost his memories. =(