So in case you missed it, Clary and Jace are brother and sister. And Valentine, apparently, had no clue he had a daughter because his first reaction is "what the fuck is this shit?"
It's interesting that this is the second time he's been on screen, and the first time he and the main character have interacted, and I'm not scared of him at all. He's less bad guy and more "Cardboard cut out". I think it's because he hasn't directly affected the main character and there's nothing particularly threatening about his apperance.
Yes, folks, we're going back to Harry Potter for a minute.
Voldemort is scary. Not as scary as, say, the Crimson King or Saron, but scary in his own way. Voldemort is about as present in HP as Valentine is in City of Bones. The Crimson King and Saron? Are LESS present. In fact Saron never appears in Lord of the Rings in person AT ALL. Part of what makes these characters scary is how the other characters act when they are mentioned. Saron is treated as horrifically demented and evil. Voldemort is so scary to the wizards, they're afraid to even say his own name. We don't learn that name until several chapters in, well after the concept of "Bad Guy" is established.
Nobody in this book presents themselves as scared of Valentine. He's just Valentine, dude of hearts and flowers. Nobody says "You shouldn't talk about that" or "nobody goes there anymore" or anything of the kind. He's presented just kind of "Whoops, bad guy" and that's it. The way other characters treat his memory indicates to us that they are not afraid of him, and so we, by extension, are not scared of him either.
The second thing that made Voldemort scary is how he affected the main character's life. He killed Harry's Parents and condemned him to live in a closet for years and years. He put the other student's lives at risk, and he caused the death of a fellow student (Cedric Diggory) before he even managed to come back to life. The Crimson King is another example of this kind of villain. He appears in Dark Tower exactly once, dead at the end of the seventh book. But his presence radiates from about the third book on, and you come to hate him for what he's done.
Valentine's actions do not seem to adversely affect Clary's life. Yes. He kidnaps her mother. But that moment feels secondary due to the plot's structure. Jace invading Clary's life is the primary conflict. Her mother's kidnapping feels like it comes third in line to the shenanigans involving vampires. So when he shows back up, you don't really care.
And last, but most importantly, nothing about Valentine is scary.
Think back, boys and girls, to the first time we met Voldemort in person. We go through HP and the Sorcerer's Stone being told how scary and awful Voldemort is. He's a bad dude, he kills people, he drinks a unicorn's blood to survive, he sets up terrible accidents to get the main character killed, and so we are primed to have our first meeting with him be awful...and he turns out to be a disembodied face on the back of another character's head.
We go from formulaic coming-of-age-with-wands type story to freaking Lovecraft. THAT is how you introduce a bad guy.
And then the second time we meet Voldemort, he's a life-sucking psychic apparation manifesting via Ginny Weasley's soul-sucked body and a mysterious book. This time we're a little more ready for it, and we are still not at all ready to go from shiny kid's story to freaking Cthulhu. And his third apperance is just as bad. After that he gets the normal entrance-and-exit moments, walking in and out of rooms and things, but by then the sense of eldrich dread is firmly established. We first met this dude as a face on the back of another man's head. He is bad news.
The first time we meet Valentine he walks into a room. We're primed for something good, but we don't get it. And because we don't get it, we have no dread of him at all.
So Valentine, Jace and Clary...talk about things. About parents and children and missing moms and blah blah blah. Apparently Valentine took Jace, killed one of the members of his circle and that dude's son to make it look like he'd burned himself to death, flipped his ring upside down to make his name's initial (M for Morgenstern) look like a W (For Weyland) and just never left the house. Also, apparently in Idris, they don't check picture IDs or even bother checking the homes of Valentine's old buddies to make sure they weren't harboring a doomsday weapon or other fugetives. I would really HATE to be a part of this world, matter of fact. It must be a breeze to get away with murder here. Oh, wait. VALENTINE HAS.
And Valentine idolizes Satan for refusing to serve. Note: The book never states what Lucifer refused to serve. God is still He-Who-Must-Not-Be-Named. And it pisses me off because now you're mentioning the fucking adversary and not discussing the heart of the entire Religion. THE STORY OF SATAN HAS NO POINT WITHOUT INCLUDING GOD IN THE NARRATIVE. It's like trying to tell the story of drugs without mentioning that you were once sober.
So then Valentine destabalizes the whole situation even more by pointing out that Clary and Jace are siblings, and this is presented as a hugely shocking thing, even though the reader figured this out ten chapters ago. Jace is all in denial because he was kissing his sister. Then we have to read Valentine's spin on the situation, which we don't care about because, again, Magical Hitler.
Luke shows up. More posturing is preformed. This is the climax of the book and everyone is standing around AND TALKING. Luke and Valentine swordfight, Luke gets stabbed, Valentine throws him on the ground and starts to stab him, Clary does the perfect woman thing and throws herself between the blade and her uncle, Jace sees that Valentine intends to kill his own daughter and enemy at the same time and stops the fight himself. Valentine tries to cover up his intentions and Clary gives the unavoidable speech about what a real monster is. Jace chooses the right side against his father. There is a fight. Valentine escapes. Jace collapses sobbing on Clary's shoulder and repeats her name over and over and over. It's all very romantic.
Not yet. One more chapter. The Epilogue. Which I'm doing here because I WANT TO BE DONE.
Clary's mom is still unconsious and in Magical Hospital. Luke is...uh, not there. Simon is supportive. Clary and Jace take a magical romantic bike ride. Even though they are Brother and Sister. Emotional closure is provided and the book is over.
THE BOOK IS OVER!