All the points you make that I highlighted are basically wrong, or assumptions.
They probably could not to synthesis from the start, They might of grown their Tech beyond where it was when they destroyed their creators. The Geth grew it's own architecture, and basically show that they were an extension of their creators, that given time, they would of grew well beyond them. This is very possibly what happened with the reapers, they killed their creators and found this way to preserve organic life from then on, if you let the Geth live, they regret the destruction of their creators, but they are happy to survive.
The Crucible was added on by every cycle, the original idea was likely far outside the box, and you have to assume that the goal was synthesis from the start, the control or destruction options were viable and likely added later. Basically just because someone is advanced doesn't mean he has all the answers, just think about reality, there was a mathematician that came from India, Srinivasa Ramanujan. He was solving things that cultures much more advanced than him, couldn't even grasp.
The whole point of the story of mass effect, is sacrifice. I beat the game today, the ending felt very much like any other point in the story, heck something very similar happens with Mordin, and just so everyone is clear, pretty sure the child is a physical representation of Shepard's mind, the kid haunts him through out the game, and makes sense that he would project the kid.
I really hope that they do give us a different ending though, something that gives us back the mass relays and the citadel, to destroy those things, is to destroy the future of the series, and I think that is why most people are mad at this ending, because there is closure, just it doesn't allow the story to continue, it's an ending in a sea of games that leave the series open for a future.