^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.