Oh some more thoughts since I think we all actually love discussing books around here, for some reason.
I liked Shran's reaction to the fact Archer is trying to baby him and how annoying he is. I think a lot of us went into this expecting Archer to be the "messiah" of the new Federation who lead everyone into the light and watching the fact that plenty of other characters are fully capable of making informed moral decisions was a nice deconstruction of how dumb an idea that is. There's no way the Federation could have survived that way.
In that, you're smarter than Tom Clancy.
I feel kind of bad the prominence of humans in Starfleet is the result of humans lucking into being the big dogs in the Federation, but it makes sense. They're the new kids around the block and no one has any real informed opinions while everyone distrusts everybody else--which, combined with Earth having a bunch of bodies, allows them to get a leg up over the other species. A leg up which never really went away.
Did you make it so the nascelles are of Andorian origin? I little about Star Trek tech. If so, it's a nice nod that not everything is Earth-based.
The nod towards Archer eventually becoming President is great but I feel very nervous about poor Hoshi, knowing what eventually happened to her in the original plans. I'm still hoping she somehow doesn't end up on Tarsus IV. It's such a tragic ending for a character who, with a lot of courage in this book, prevents a war.
(Nice job giving something for Hoshi to do)
Possibly my favorite part of the novel now that I think about it is Doctor Phlox's talk about how one of the biggest things you have to do is let go of the past. A lot of fiction glorifies revenge or utterly crushing one's enemies. In RL, though, you just have to let go the memories of war and move on. It's probably why Living Witness is my favorite episode of Voyager.
Also, a good bit about how his race disagrees with the genetic engineering ban and how Earth got that done with everyone but them. It's a nice bit of political truism that, sometimes, things get pushed on through without any serious debate that only hurt people who aren't large enough to argue.
Are the Space Whales related to the ones from Star Trek IV?