Despite killing thousands of civilians on Kolthas Station, Cassius actually didn't commit a war crime since it was attached to a military depot. The civilian section was destroyed but that was a function of it being built into the same location and having interdependent life support. If anything, the Commonwealth was hiding behind civilians. Not that Cassius views it that way.
Cassius choosing to go Screw This, I'm Outta Here! makes sense given both the Commonwealth and the Free Systems Alliance have screwed him over repeatedly. The only people he cares about in the world are on The Melampus.
The fact Ida is unable to keep control over her crew and most of them join Cassius in The Mutiny makes sense with the fact that he's a famous figure, they're in the middle of a war, and she's been revealed as having used them as a spy vessel without their knowledge. Ida recruited a Ragtag Bunch of Misfits and none of them are interested in joining the fight on either side.
The revelation that Cassius' doppelganger is actually his father makes perfect sense with the fact that not only is the other Cassius a brilliant politician as well as loyalist to Crius but he's also Armchair Military that never goes out to fight. Cassius was neither an inspiring leader or particularly loyal to the Archduchy. He was only a spectacular starfighter pilot. His father, by contrast, was the former leader of the Archduchy and its Evil Chancellor. It makes even more sense with the fact that Cassius is a clone of his father.
Cassius the Elder cloning himself despite having two heirs already makes perfect sense when we meet him and discover he's a raging narcissist.
The Elder Races are completely unstoppable and completely arbitrary. They may choose to wipe out the Community or humanity on a whim or set up a terrifying war. They are Abusive Precursors that are also Chaotic Evil rather than Lawful Evil. You can't even appeal to their logic.
The destruction of the Kathax Prime's temple means that the entirety of the Kohlan race that was Brain Upload-ed to survive are now extinct.
Cassius managed to kill two of the Elder Races in Lucifer's Nebula while Zoe managed to do a Brain Upload of her mind. What will this mean for humanity?
The statement the Elder Races are the "Great Filter" of Fermi's Paradox means they are responsible for the deaths of millions of races.