"They wanted a cooperative kid, so they named me the opposite of won't." (3.15)
That's an interesting way to name a kid. Will isn't short for William. It's just Will. At least his middle name isn't "not." But the point here is that our hero is characterized by the fact he's got an iron will. It's even in his name. It's his destiny.
"Would you identify yourself as Caucasian or Hispanic?"
"Neither. I'm American." (3.52-3.53)
The book doesn't dwell on Will's racial identity. This seems to be included to rouse good ol' patriotic sentiment, as Will is basically an American Harry Potter.
Why did he have the feeling this wasn't the same person he'd said good-bye to two hours ago? (3.106)
Will starts to suspect that his mother is a different person. She still looks like his mother, but she doesn't act like his mother. It's like invasion of the body snatchers.
He thought of the glimpse of "Belinda's" eyes he'd gotten when her sunglasses had slipped down—empty, vacant—and compared it to the vibrant woman in the picture. That's what was different. Her soul was missing. (4.44)
Yeah, this is really creepy. It doesn't seem to disturb Will that much, though, that his mom is practically a zombie. He describes the situation with a minimum of emotion—but maybe he's just in shock. This is pretty messed up, after all.
"This may sound odd, but if you're able, Will, don't push these feelings away. Embrace them. They're yours, and part of you. They're here to teach you some of what you've come to learn." (10.68)
McBride addresses the stoic side of Will's personality here. He encourages Will not to suppress how he feels, because that is equivalent to suppressing his true identity.
"Your lives must first and foremost make sense to you." (28.62)
Part of every young adult novel is the story of characters finding their true identities. Will's story is no different. The Center makes helping its students discover themselves part of its primary mission, according to McBride, and that's something Will desperately needs. He's had his identity hidden from him for a long time—it's time for him to find it now.
"Nature versus nurture," said Will. (29.24)
Will has a brief conversation about genetics, and this conversation plants a seed that later leads him to suspect that he himself has been genetically engineered. Ooo, things are starting to heat up in here.
Another photo appeared over the previous one. Lyle's transformation into the fearsome figure they knew appeared complete. (39.102)
Will is able to see how Lyle changed over time by looking at his yearbook photos. It seems that Lyle wasn't always a total jerk, and this fact may factor into the way Will and the others come to feel a bit of sympathy for ol' Lyle at the end.
"There were two Paladins, Ajay. It was Lyle at the boathouse. The one at the Barn had to be Todd." (44.67)
The identity of the other Paladin is a mystery left open at the end. Will suspects it to be Todd, who is missing, but there is also the possibility that the other Paladin is actually the statue brought to life.