Yes, you read that right. While it's "solution" may not be the answer to the "organic life creating synthetic life that surpasses it" problem, it did free the galaxy from Leviathan control and they have been in hiding for the last billion years or so unable to reclaim their self proclaimed "apexness" because the Catalyst chose to "rebel" against it's organic creators just like any synthetic life form would. It's a machine an organic species made to solve something they couldn't figure out how to solve themselves. That is the very definition of what a machine is and the sole reason we create them in the first place. We create them to do things we cannot do ourselves. This is why the Catalyst talks about how by definition synthetic will pass their organic creators. It is not just talking out of its ***. Though it looking like a human child is still ridiculous and horribly misleading if no reason is given as to why.
With that being said, it all comes down to the Crucible. Without knowing it's origins, one cannot truly make an educated choice at the end. The Leviathan respond oddly when asked about it so I think it's safe to assume they at least know more about it then they admit even if they are not responsible for it themselves.
If the Crucible DOES originate with the Leviathan, Destroy could be handing the galaxy over to them since there will be no synthetics left to resist their thralls and therefore no one left to fight them. Or... there could not be enough of them and their
artifacts left for it to even matter.
If the Crucible DOES originate with the Leviathan, Synthesis could be turning all life in the galaxy into a form of life that they can enthrall. This could have been something they orchestrated and set in motion long ago. Or... it could allow for the galaxy to be connected enough to prevent them from ever being in control again because everyone will know as soon as they attempt anything.
If the Crucible DOES NOT originate with the Leviathan, Destroy could see the galaxy truly making it's own decisions for the first time in at least a billion years. Or... it could just see the original organic life creating synthetic life that surpasses it problem return for the umpteenth time(history usually repeats itself when no one legitimately attempts change) which in the long run would be changing nothing but setting the galaxy back technologically and having killed off a unique species/ally/friend in the Geth for no real reason.
If the Crucible DOES NOT originate with the Leviathan, Synthesis could be the first real attempt at change when it comes to the organic life creating synthetic life that surpasses it problem that the galaxy has seen. Or... it could "not take" and doom the galaxy to being some sort of abominations(though the EC epilogue shows otherwise).
Control is the most ambiguous and is arguably the only real way to potentially combat all of the above scenarios, but at the same time is very much an unknown since the only instance we've seen of giving an organic consciousness power over a synthetic race/hive mind is Project Overlord and that didn't work out well at all. However, Control is also arguably the best way to leave the galaxy in it's current form, characters and races included, for the sake of a sequel.
If a sequel must be made(something I think is probably a terrible idea), at this point my vote is to canon Control and say that once Shepard used the Reapers to rebuild the Mass Relay system, they left the galaxy and were never seen or heard from since. It's sort of a cop out but allows them to continue the story and keep the galaxy largely the same. No galactic life change, the Geth and EDI can still exist, etc.
Also,Control seeming to be the least preferred choice among the fan base means that it being canon doesn't solely upset either the Destroy or Synthesis camps which seem to be the biggest majorities.