Despite the glowing green eyes and skin, I believe this was the best choice. Especially after all that drama between quarians and the geth. I'm not gonna be like "Sorry guys since you're synthetic and even went through the trouble of sacrificing Legion to make you guys intelligent plus brokering peace between you and the quarians, I'm going to have to kill you guys too."
Ugh, I'm sorry, but I still consider Synthesis to be the WORST "good" ending, thematically and from a narrative perspective. It completely flies in the face of ME's previous Diversity Makes Us Stronger and Genetics Aren't Everything messages in favour of a Peace Can Only Be Achieved Through Uniformity and Genetics Uber Alles theme.
Plus come on! Since when were glowing green eyes ever a good sign in modern day fiction?
I have to admit, I don't know. It could be that it was the only way peace and understanding could be guaranteed within the parameters defined by the sentient races' cultures at that particular point in time.
How? Genetics don't work that way. It'd be like suggesting that the Crucible inserted a "Peace and Love" gene into the galactic population.
Besides, Shepard already demonstrated that Synthesis wasn't necessary -- the quarians and the geth were co-operating and on their way to co-existence long before the Crucible was fired up. Especially as the geth were completely uninterested in wiping out organics. Deleted audio of a geth prime on Earth even reveals that the geth find "synergy" when working in concert with the quarians. EDI, likewise, has already placed herself firmly behind the rest of the galaxy against the Reapers and was coming to understand humanity on her own terms.
Plus you have to admit this: if every husk suddenly became conscious and self-aware, what does this mean for husks who were fused to other husks? Such as the guns for cannibals, which are made from humans fused to their arms? Or brutes, who are two creatures with different DNA chemical structures literally bolted together (you can actually see the krogan's exposed ribs)? Adding to this, do you think many of them would want to remain in that state, as twisted and malformed as they are? The Reapers had little interest in ergonomics; it's highly likely that they'd be in immense pain and suffering from how crudely they were fused together.
"How? Genetics don't work that way. It'd be like suggesting that the Crucible inserted a "Peace and Love" gene into the galactic population." Oh, derp, I guess I left out any indication of what exactly I meant. That is, that some or many of the cultures could not achieve lasting peace and understanding without their perspective being changed by the awareness that they share DNA with the other cultures.
Your second and third paragraphs make the points I have no good answer(s) for. Frankly I prefer Indoctrination Theory to all of this space-magic dren.