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Because the only way it makes any sense is if everyone had their minds rewritten.
No one has any problems working with the Reapers, EDI apparently needed Synthesis to feel something she already said she felt, husks are now sentient, and Wreav doesn't start a new Krogan Rebellion like he does in the other endings.
Bcause it is being forced on everyone, instead of getting there on their own. And not everyone would be happy to the change. The council races may be fine with it, but what the others? The Batarians probably would not like the idea of their dna now being the same framework as the others and I don't think the Geth would be that happy either, due to the fact that they wanted to reach understanding on their own terms. Plus what about the pre-spaceflight races in the galaxy? If they woke up one morning to find everyone now had green eyes and circuitry on their skin there would be blind panic by some of them. And as the poster said above, What of the Reaper forces? If they gain sentience, do they regain the memories of their past lives? Imagine if that was the case, and how horrifying that would be for the individual.
"Dad, mom said you were infertile, so how was I born?" "Nanomachines, son."
I dislike Synthesis because of five reasons: 1) Its the type of "evolution" that Saren wanted in the first game. 2) Its Shepard choosing this for the entire galaxy by himself. 3) Shepard dies. 4) The Reapers still lose on THEIR terms. 5) Its a massive shortcut for organics and synthetics to "co-exist" with each other rather than working out differences and actually adapting to one another.
"Theres power in stories. Thats all history is: the best tales. The ones that last. Might as well be mine." Varric