You may not have intended the reader to make a Marty Stu connection, but virtually everyone else has. Here's an example of a pretty good review that covers the highlights.
http://xodiac.fo.cx/rev/view.php?bookid=996
Most rational folks would see a mostly Marty Stu main character, and the rest of the book being essentially a commentary on how you think the War on Terror should be run.
I gather your live fire exercises weren't green third world troops, still learning their systems and equipment? There's a mild difference between trained soldiers that have been around the block a few times and green recruits. I was generally taught crawl, walk, run. Throwing "newbies" into the run stage rarely worked out as well as expected.
I never considered RSO's as a "shadow chain of command", but extra set of eyes that has nothing else on their plate but ensure no one was about to die unnecessarily. Calling RSO's a shadow chain of command is kinda insane at best. I'm quite sure there are bad RSO's that "confuse" troops and make things unsafe, they obviously need either training or a different slot. The ROLE of RSO should be to facilitate training while improving.
They can do that. Nothing to be done about it. And if they want to do that, meh, No skin off my underendowment.
Where did you see that they were still learning their equipment? Oh, that's right, you didn't because, instead of reading the book you decided to rely on heavily redacted hit pieces (though I liked Doug's review, at least, told him so, and advertised his site on my conference on Baen's Bar).
You can consider it what you like. What I consider it is immoral, unethical, cowardly putting up of mere forms, entirely for purposes of CYA, while a) increasing the danger for the troops, mistraining the troops, and c) undermining their confidence in their own chain of command, hence further mistraining the entire unit. I do, in fact, know of people killed because there was a second, shadow chain of command. 2/34 Infantry, circa 1983, Fort Stewart. In effect, when you make them responsible they will take responsibility. They will give orders. They will have the troops guessing who the hell they're supposed to listen to. If you haven't seen that then you haven't been paying attention.
Just out of curiosity, what's your MOS, your units, and your general level of experience? Who knows, it may, in theory, exceed mine.