Narm Charm: The MASSIVEGambit Pileup can get a bit ridiculous at times, but it makes the novel all the more entertaining.
Strawman Has a Point: Despite their Jerkass tendencies, Smug Snake demeanor and terroristic practices, the Insurrectionists do have at their core a few legitimate grievances with the UNSC. It tends to get lost, though, when you consider that the UNSC is actively trying to protect colonies that are neutral or even hostile towards Earth's influence (and getting the crap kicked out of them for their troubles), whereas the Insurrectionists care only about their own turf and place a higher priority on starting a civil war than on resisting genocide.
What an Idiot: The inhabitants of the Rubble make a deal with the Jackals for their survival. They assume they could make a deal with the Covenant and possibly even join. This despite the fact that the Covenant destroyed Madrigal, from whence most of the refugees came.
Averted in the fact they have an escape plan just in case it fails.
The Elites Honor Before Reason is taken to this level. Thel, who is the Sole Survivor, is so shook up by the events (particularly the fact that the leaders he so zealously followed are very much mortal beings with materialistic desires and having to kill his best friend) that it basically kick-starts his development into the warrior who would eventually become the Arbiter.