Rather than the whole "synthetics will kill all organics unless we stop them from being created" it would have made much more sense that Leviathans created the first Reaper as their way of "ascending" to a higher plane. Becoming immortal, even more god-like, or they did it because the universe at the dawn of time was far more hostile to organic species. Whatever, that does not matter. They are arrogant enough to try that from what we know about them.
So they create the first Reapers, Harby and a few others but something unexpected occurs. Rather than becoming smarter, more powerful they get stuck, unable to evolve past what they are unable to create anything new they stagnate. Then considering the way they were created they decide that maybe they need "fresh blood". New civilizations, new species to join them in their techno-organic "ultimate" state. So they go around the galaxy harvesting lesser species. When that doesn't work they try to harvest their own until extinction.
A few dozen cycles later they worked out that the only species that offer something new would be species that have reached a certain level of technological progress. So they create relays, Citadel and start the cycles as we know them. Every 50k years before the civilizations are too much of a threat to them they harvest the advanced ones and then retreat. All in a hope that with enough numbers the final solution to attaining god-hood would form.
This way the arrogant speaches from both ME1 and ME2 have their full weight. We still have the cycles, still have some kind of "higher purpose" that Reapers think they serve but it still allows the idea to remain grounded.
Same choices could be presented(with variations upon each depending on EMS), destroy but without killing EDI and geth(if EMS high enough)
Control-literally the same thing but shepard doesnt die if ems is high enough
Synthesis- yeah I've got nothing. Maybe something about letting reapers go? Or something like using the Crucible attached to the citadel as a giant download thing, downloading the "core" intelligences of Reapers into the superstructure that is Citadel+Crucible creating this way what Reapers had been trying to but then jumping the whole structure into dark space where they can do no harm?