I think what bothered me about the Vanguard-series up to that point was the moral ambiguity by the SF-characters. T'Prynn and Reyes' actions against Pennington were just despicable. There's no other word for it, even if they might have been warranted by the situation/orders/whatever. And of course, the willful ruination of a person happens in reality "for the greater good", but that's why I read Star Trek because I kind of like to have the illusion that society can grow above all those petty, immoral decisions (not withstanding that DS9 already started to darken that illusion by Section 31 or even Sisko's actions). So I really appreciated the show conscience on Reyes' part especially, but also that this show of conscience - not in the least caused by the terrible choice he had to make surrounding Gamma Tauri IV - had consequences for him in return.
I enjoyed the events on Jinoteur (even though Sagitarius' crew is a bit... quirky for me. There are only so many one-liners I can stand.) very much, especially now in retrospect after having read Open Secrets. Who's really the bad guy among the Shedai? What's the Apostate's agenda? I thought it very interesting that SF is viewing the Apostate as some kind of good guy, whereas for the Tholians (Nesrene) he's the absolute evil as he was the one to enslave them. Again, at least that's my impression from Open Secrets.
Overall, I felt as though the plotthreads start coming together. With Marcus' appearance it becomes clearer what the meta-genome is about. The mythical Shedai come out from under the shadows, the race for mastery of their technology between the Klingons and the Federation is on (with contributions from other races), and the main SF-protagonists so far (Reyes and T'Prynn) were given a heart and a conscience fighting their own demons - literally and figuratively.
Great book - definitely the turning point in this to me so far lackluster series (when I first read it, not when I went back to the opening books - what a change in impression a few more details can make).