Part of the weirdness, I think, is that you can control just the Reapers...or you can wipe out all synthetic life? How is that really an equivalent choice?
Wiping out synthetic will protect the organic (i don't buy that argument), but harvesting the organics is the reaper's weird way to preserve a species (i don't believe it does, as the species no longer have free will). so either way, it's a bunch of baloney.
He didn't.
When humans finally put the citadel inside the crucible, they have check mated the reapers.
Remember somewhere in the game, it is said that reaper uses the mass relay to guide how technology advances (I think this is correct,correct me if i am wrong), so it's totally within Reapers's plan to allow the lowly organics to think they are creating a superweapon to defeat the reapers, when in truth, it does nothing. They just want to bring the dominate species the ultimate despair when the crucible does not work as intended.
Disclaimer: Nothing I said make sense anymore. I am going to bed