ok first love your story, it feels fresh & well thought out.
Ok I had this thought, A bout the quarians something I thought you may be able to explore.

ok here it is. quarians need to keep them self divers in order to prevent the consequences of inbreeding. such as preventing birth defects. so do you think I kind of Eugenics program would exist in order to mantane this.

this leds in to a Question how do the quarians deal with Birth defects? or mental disabilities? they can happen so in order to prevent or at lest lessen this possibility Eugenics  would be necessary.

To a third point how would they deal with crippling injury like losing a leg or arm or brain damage?

I think the quarians would practice euthanasia to prevent the strain on the Fleets strained resources same with birth defects. it makes sense considering the state there race is in all must contribute to the fleet in order to survive, so what if they can't? what if they lose the ability to contribute? 
what is they never could?

that what I have so fare, I hope it makes sence.