First off, the idea of this novel if just fuckin awesome. Great way of showing the science behind how something like a Nocturnal could even come to be.
Thing is, I think you did a good job of trying to expalin the subculture of the Nocturnals, showing the Grooms Walk, showing Mommie, showing how the King (Rex and previous King's) were escaped due to the crazy old lady, and showing how that worked first with Bryan and how that will work in the future with the kid that Aggie James snuck out.
Only problem is it feels like all of that information was discussed 20 epsisodes again and was never really addressed again. In many of your stories, you continually go back and forth between the different plot threads to keep all these people together, ultimately culminating in a huge train wreck where all these threads meet.
I really wish you interspersed more about Mommy and the underground throughout the story. I have to say that Mommy and those mutant kids is way scarier than the grown up Nocturnals. I don't really have a good feel for who Marie is, how she really got there, what she's thinking (if she can think) and what her role is (anything more than a breeding ground).
Is the kid that Aggie helped escaped not to be continued in the story? Was that merely a way for Aggie to escape his self-torture and move on from a drug abusing bum to a decent person again?
Just seems like all those side stories should be more interspersed. I hear what you're saying about having to take out a bunch of words to get this to press. I'd say you should even think about stopping somewhere around Robin's death and just go into more detail about Aggie, Marie and those plots.
Start the 2nd book right after the death of Robin, and the 2nd book could probably even go a little bit passed the battle on the ship.
Just some ideas, would be cool to hear what you think of them.