You don't even need to get into the fact that Star Trek should be about something,
Didn't you
just cite the 9/11 Truther bullshit? It's
about that. Specifically, Orci used his weird political fantasy as fuel to tell a story about untrustworthy powers that be rigging the game to allow for their warmongering. It's about that, with the typical subplot about making sense of your emotions that gets dragged out every couple years in Star Trek in some form or another.
Again, it's pretty clear. It's not complicated or obfuscated. I think 9/11 Trutherism is fucking horseshit, and Orci is a jackass. But the kernel at the core of that repugnant real-life theory can be (and was) transplanted to a sci-fi setting and they built a story around that, incorporating Khan for those purposes. Kirk's sacrifice is unearned, and the last reel of the film is really messily/sloppily glued on. Spock Prime should never have appeared (and Spock Prime shouldn't even exist, the series should have been a flat reboot, and almost all the films' problems stem from taking half measures on that front and having to address Spock Prime's existence), but again - the film's a Starfleet conspiracy story, and a pretty straightforward one. It's not about nothing.
Space Seed is a basic Noble Savage story that ends with Kirk beating Khan with a pipe before marooning the man on a planet with his crush.