"As a galaxy we can now live the lives we wished for, where organics and synthetics can coexist peacefully. With peace across the galaxy and unlimited access to knowledge to recover the greatness that was lost, and surpass it, as the line between synthetic and organic disappear we may transcend mortality itself, to reach a level of existence I cannot even imagine."
I really don't understand people can interpret that as there being room for some form of conflict in a post-synthesis world. There's no need to fight over resources because you have millions of years of reaper knowledge to tap into to find new renewable resources. EDI says that they can transcend mortality, so what's the point of war if you all can live forever, without want or need. Your also still forgetting that if there's any conflict that would threaten the utopia that was just created, well you still have an army of Reapers that would more than likely fight to preserve their new found harmony in the world.
"You will die. You will control us but you will lose everything you have. Your corporeal form will be dissolved, but your thoughts, and even your memories will continue. You will no longer be organic. Your connection to your kind will be lost, though you will remain aware of the existence. We will be yours to control and direct as you see fit."
"Eternal. Infinite. Immortal. The man I was used these words, but only now do I truly understand, and only now do I understand the full extent of his sacrifice. Through his death I was created, through my birth his thoughts are freed. They guide men now, give me reason, direction. Just as he gave direction to the ones the followed him, the ones who helped him, achieved his purpose, now my purpose. To give the many hope for a future. To ensure all have a voice in their future. The man I was knew he could only achieve this by coming something greater. There is power in control, there is wisdom in harnessing the strengths of your enemy. I will rebuild what the many have lost. I will build a future with limitless possibilities. I will protect and sustain, I will act as the guardian of the many."
At least to me it's pretty clear Shepherd isn't the sentient being in control of the Reapers. If you want to debate that, sure but it's also pretty clear he isn't going to fly off into the sun so it brings us to what others have said about this problem. If you have a major conflict within the control universe you have to either give some explanation on why the said conflict isn't seen as important enough to a race of machines who were imprinted with the essence of the guy who did everything he could for everyone in the galaxy from helping people cross the street to saving them in a combat zone. Even more problematic you have to introduce some Deus ex Machina in the form of some device that would inhibit or stop shepreaps from intervening. The introduction of something like that would most likely have the plot implode on itself because it will leave most wondering why was civilization piddling around with the crucible when this item could of been found/created. There's also a point to be made in line the synthesis ending. Shepreap says he will rebuild, so why wouldn't he also tap into the millions years of collective reaper knowledge to assist civilization to the point of utopia?
The headcanon needed to not have either universe be a happily ever after is too strong really. If you took Destroy as canon we could actually have a story about creation and not destruction. Rebuilding the galaxy, one scrappy adventure at a time. It would allow for a DA:O style play with protagonists from a multitude of species and none of them have to be a tough as nails soldier, each with their own act 1 to play before getting to the big stuff.
- Batarian trader turned leader trying to rebuild their nation and dealing with hard subjects like slavery.
- Krogan surveyor trying to find a new planet for expansion and having to negotiate with other species who are wary of such a move.
- Human diplomat trying to rebuild the council now that citadel is in Earth's orbit, but there's still plenty of problems in galaxy.
- Asarian artist/scholar trying to find what was lost in the war and re spread their culture now that it's been ground into dust.
- Salarian smuggler struggling with trying to go legit along with the rest of Omega as it overnight becomes the galaxy's biggest trading hub.
Even these smaller conflicts wouldn't have a place in a control/synthesis world because either shepreap would already have the answers to everyone's problems, or that the synthesis utopia would have already solved these problems without friction.