Now see, I think the plot makes plenty of sense, in that it's two biased factions acting out their biases violently in the hopes of coming out as dominant and getting their way, A.K.A. every war ever seen by mankind.
CGs want to protect Earth and humanity, hate Homeworld for both holding opposing viewpoints and taking a stance against personal shit like fusion. Homeworld wants Earth gone since it's not only useless, but an active threat/base for threats, and the CGs took out many soldiers in the past during their massive treasonous act.
If you want to talk about shit that makes no sense, how about we talk about the hard-on for humans the CGs have, despite all proof to the contrary regarding their worth? I mean, all of this shit that's happened so far, including many giant monsters, a huge number of mystic sites that should be accessible or at least visible to curious humans, and even an actual full-on invasion of a resort town facilitated by a massive ship, which should have been so visible that every world government would be watching while sweating profusely. And yet, no human response to any of the insane shit going on, none whatsoever?
Humans just plain don't have any strength, intelligence or even simple self-preservation instinct in SU. No one ever tries to fight things, no one ever freaks out about aliens, no one even raises a goddamn eyebrow about anything unless the plot demands tension. In any sane universe, humans would go nuts over an alien invasion, and some sort of armed force would attempt to acquire their tech/fight them off. And yet, humans just don't care, no effort to fight back, no effort to understand or look into anything, not even a basic inkling of fear for their lives or shock regarding the events happening around them. They're practically walking goddamn shrubs with no conscious thought.
Why in the fuck did Rose want them protected again? An alien boner for an individual specimen?