^Wow. I agree that the destruction of the Omari Ekon should have been covered better. It was such a major player in the series that I feel its destruction meritted a chapter of its own rather than a passing mention. But on the other 2 points, I couldn't disagree more.
If the Enterprise hadn't entered the fray, every one of the main characters would have been killed. I honestly wouldn't have believed them winning, nay, surviving, with the resources they had at the beginning of the battle. Besides, with the Enterprise being prominent in Book 1 and the series shedding light on TOS throughout, I find it appropriate the Enterprise should be there in the end.
I don't understand how you come down so hard on Reyes. If Nogura had been commanding during the Shedai massacre, he would have given the order to glass the planet without any visible remorse and definitely wouldn't have leaked information. Reyes tried to convince his ex and her people to not turn down UFP support and she wouldn't listen. He then tried to warn others of the Shedai threat and was crucified for it by Starfleet. The burden of those deaths go to Starfleet command and Reyes' ex.
I feel Reyes and Desai did their share of suffering and I was happy they got an appropriate ending. I further appreciate this knowing that in the beginning of the creative process, there was no plan for Reyes to face court martial at all.
I have no problem with the Enterprise showing up the first time, helping out with the Sagittarius mission. Spock also got his time with T'Prynn back on the station, bringing their story to a close.
It's having the Enterprise show up and save everyone that felt wrong. The whole "Gosh, if it weren't for the Enterprise we'd all be dead" moment. Having someone from outside the Vanguard series save everyone at the end just felt wrong to me. It's the final curtain. Let the stars of the show have the spotlight without the better known guest stars upstaging them.
Reyes let civilians go to a place that he was very sure would prove to lead to their deaths. The only one he seemed concerned about was his ex-wife. If he had told them that the situation was extraordinarily dangerous due to a poorly understood, hostile alien race and they went anyway then it would be on them. He didn't. He denied them the knowledge to make the choice for themselves and let them get slaughtered. And then he didn't face any sort of punishment for his actions. He got court martialed for revealing secrets. Letting him live on with the love of his life on a peaceful planet lets him escape the consequences. Actions, particularly ones that lead to hundreds of deaths, should have consequences and he totally dodged them.
Another thing I found interesting was that TOS was essentially set during wartime, albeit on a limited scale in the Taurus Reach. The revelation that Kirk was seeking out powerful allies to take on the Shedai was very interesting. Was Starfleet looking to use M-5 controlled ships to combat the Shedai? Did Starfleet have Bailey try to recruit Balok and the First Federation to join the battle? How many episodes can you tie back into the Shedai war, even indirectly?