Looks like I'm overruled!
I still think a lot of this feels very contrived, so let's fix that.
For a start, let's call the section Universal Special Rules, not Special Qualities.
In the ship profile, write whatever makes most grammatical sense. E.g. "This ship is Massive or This ship has Augmented Damage Control" rather than "This ship is subject to the Massive quality". Saying something has 'X' quality is less neat than just saying something has 'X'.
Names of these USRs. In particular, I think the following names should be changed:
Limited Fuel. They don't really have limited fuel. This is more a case of Inefficient Thrusters.
Improved Augers. Even in 40k, use of the word Augers is rare, so many people won't intuitively know what this means. Also (though I'm not certain), I think Auger is a drilling device whilst an Augur was a priest who interpreted the will of the gods, making the 'u' spelling more appropriate. Use Improved Auspex or Improved Auspex Array instead, as that is more common in 40k, and the addition of 'Array' makes it immediately clear which system is being referred to.
Terminators. Nothing really wrong with this name, except that it leaves out any possibility for Nids, Eldar, Dark Eldar, Necrons, Orks and Tau to use it. Perhaps Elite Boarding Parties.
Apex of Technology. So what if it's the Apex of Technology? The key quality is that the race is willing to destroy it rather than let it fall into enemy hands. Guarded Technology or similar.
Elite Cadre. Wince. Regiment Embarked.
Hunter. No escort is nimble enough to keep up with AC, and what is it about a Bombardment Cannon Shell that makes it a Hunter? Flak Shells or Flak Storm.
Bombard: Is it really necessary to spell out the rules for individual weapons systems in the USRs? Why is the Bombardment Cannon singled out for special treatment, compared to say the Pulsar or Sepulchre? It's OK to not have a special rule for everything.