I'm not certain which DLC it is (I think Citadel, maybe Leviathan), but the Catalyst stops directly referring to the destruction of the geth and EDI during his spiel about Destroy. He does say it won't differentiate between Reapers and 'regular' synthetics, but it does stop specifically stating that the Geth and EDI will be destroyed along with the Reapers.
To me, Control is too likely to end up proving Lord Acton's Dictum (Power corrupts; Absolute power corrupts absolutely). No matter how pure Shepard's motives, no matter how much of a paragon she may be, in the end, having complete control of the Reapers (and thus the direction of the galaxy) would corrupt her. Yes, she may have the best interests of the galaxy at heart, but how long before she starts deciding what those best interests are? What happens when she no longer has the emotional checks on her power that her crew/LI would offer? One hundred years? One thousand years? What happens when Shepard no longer remembers what it is to be alive?
Synthesis is just hogwash all around, for me. For one thing... space magic. I know we're dealing with high sci-fi here, but I just seriously have trouble wrapping my head around the idea that the catalyst can suddenly turn every living species in the galaxy into some biosynthetic organism. And frankly, I don't understand how the Crucible/Catalyst can have that kind of power and control, and yet somehow when it comes to Destroy, it can't differentiate between biosynthetic organisms (the Reapers) and pure synthetics (Geth/AIs)? Furthermore, the entire time you're going through ME3, countless comments are made on how good diversity is, how good multiculturalism is, how important it is that the galaxy is filled with diverse species working together... (Play Beyond Ashes and listen to Javik explain the differences between his cycle and our own). Now suddenly, we're supposed to believe that diversity is Bad and that obviously the absolute best choice is for everyone to be the same?
Sorry, I can't buy it.
I support headcannon. I support Destroy and I support Shepard living on after the breath. And frankly, I support the idea that if the Crucible/Catalyst is so dang all powerful, it can tell the difference between a biosynthetic and a synthetic. Yes, in my headcannon, the Geth survive. Maybe I'm wrong for supporting the concept of a happy ending, but then, I don't play games for realism. I play them because I want to enjoy myself, and I don't enjoy seeing hundreds of hours of work turned into nothing more than a smear of color. *shrug*