A big part of the problem (and there are many, many problems...) is that I have no idea what synthesis actually does. Everybody has some glowy bits, but what does that mean for them? What does being part-biological mean for machines? Are all machines now part-biological, or just the self-aware ones? If it's only the self-aware ones, how? Is the Normandy now partly biological? Why did you need Shepard to jump into a beam of light to activate it? Since when was a machine that could rewrite the DNA of all living things - and introduce DNA into non-living things - even something that could exist in the Mass Effect universe?
And what about destroy? What qualifies as a synthetic? It kills reapers, I guess. And geth, probably. EDI dies, or just her robot body? If EDI dies proper-like, what about the Normandy itself? What about VIs? Are they destroyed? Are all machines destroyed? What was that shit about "you have cybernetic parts too, Shepard"? If the Reapers were made to prevent people from creating synthetics that would destroy everything, yet they had a device that could destroy all synthetics everywhere, why didn't they just use that instead?
And why are these all stupider versions of the ending of Deus Ex?