I think Clockwork Princess is so effective because its plot works to highlight how far the characters have come since Clockwork Angel. On this reread, it really stood out to me how soul-crushingly lonely they all are at the start. Tessa has lost everything, Will is lying to everyone, and Jem won't let himself get attached to anything. The three of them (plus Charlotte, Henry, Sophie, and Jessamine) are all together at the London Institute but none of them ever communicate with each other, so they still feel crushingly isolated. Even Will and Jem, who are clearly the most emotionally intimate of the group at that point, have a constant barrier between them. Jem knows that Will is lying to him, and he's content with that but it still weighs on them both.
By the time of Clockwork Princess, everything has changed. Jem and Tessa are engaged, Will has told everyone about his curse, and Jem even knows that Will is in love with Tessa. Charlotte and Henry are finally aware that their love is mutual, Sophie has spoken up about her desire to become nephilim, and the Lightwood brothers are reconnecting for the first time since childhood. Their feelings are complicated, but because they all know about those feelings they're able to protect each other. The main trio are physically isolated from each other for most of the book, but that distance doesn't matter because they're truly emotionally connected for the first time in their lives.
Because Clockwork Princess separates Will, Jem, and Tessa from each other; it pushes them all to openly admit their most desperate emotions. They can't hide their feelings anymore, and it becomes painfully clear to everyone involved how much they all love each other. The fact that Mortmain can pull them apart physically without crushing their drive to save each other proves exactly how far they've come since Clockwork Angel. They may not be together under the same roof anymore, but they're closer to each other than ever before.
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