Here's the way I see the choices and why those are the choices. I think the crucible functioned just to use the citadel and relays to send out a sort of emp like pulse throughout the galaxy to destroy the reapers. That's the only way to kill them all, really, so it has to use the relay system. Also, the kind of clue and crux to me about the crucibles use is Javiks absoluteness of being against any synthetic. He is against any compromise. Kill then at once, and kill them all if you can. This is the clue to the crucibles main fiction; kill them all at once and be done with it.
Anyway, the relay system and citadel is cared for by an overarching ai/vi sort of reaper (star child). Now when you meet him your intent is to use the crucible the way it was meant and destroy everything. Obviously anything the kid says is going to be from his perspective. Remember he has a deeply differet perspective than you. He's seen millions of years of evolution of both synthetics and and organics. Essentially he's kind of from the future but not really. Anyway, anything he says is reaper logic. And by reaper logic he is correct, since they consider themselves the sort of ultimate in evolution, and they came to the conclusion that the imperfect and chaotic organics had to be assimilated into their perfection. Since they believe they are destiny, then yes they would say that it is inevitable to happen again and again down the road. Remember the geth and edi are a sort of micro on the scale of time that it would have taken for the reapers to have come about. They're further back, so their peace is temporary according to the reapers.
Anyway you're given other choices, but those choices are jus a sort of modification of the original use of the crucible, so they have to follow the same sort of rules, thus the similar endings. Synthesis is presented as a solution to the problem of imperfect/perfect conflict because afterwards they're all the same and all perfect and have order. Control is given as an option, because, I think the reapers believe that once Shepard does this he will essentially be a reaper. He'll be one of them. He'll be enlightened to their logic and their cycle. Ultimately they don't care about being controlled, likely because of this. Also, control is like a self preservation option for them. The clue here is the past indoctrinated always argued for control.
Anyway, you can destroy them as you intended, but you're warned that this would destroy a lot more. Remember, the basis for technology throughout the system and especially the delays and things were reapers tech. In destroying reapers they destroy it all. You could also think of that sort of thing as a fail safe for them. That's why Shepard is warned by the star child. It's like when you're persuading someone you'd say sure you could do it that way, but look at the consequences. And then the star child added in his own logic and perspective along with that persuasion that the cycle would continue later anyway. Anyway, to sum it up easily he's basically saying "well you could do what you originally intended, or you could use the thing in the way I've modified in these ways because of my perspective. "
