@mcsupersportWell, I agree with a lot of that.
You're right that the whole synthesis thing is a plot problem. But it's obvious to me that they didn't put a whole lot of thought into it. It seems they started with whatever this "dark energy" plot sequence was going to be and either ran into a plot... wall? Or realized implementing the plot would take more time than they were willing to invest and wanted a quick pay-out. So, they quickly chose a simpler, cheaper plot... even if it didn't make a whole lot of sense.
You're right. Synthesis? The god child? Really? They had to know that implementing such ludicrous story points would change the fundamental nature of the galaxy... but by that point it was too late. Changing it again would require a release-date delay and cost them money. And this IS EA after all.
If they're going to come out with a new Mass Effect game taking place after ME3 in the timeline, it'll likely be whatever is considered the proper canon choice. Destroy I believe it is.
So, unless the writers can come up with some clever method of dealing with it, the other methods, control, synthesis, and the refusal options will all be conveniently forgotten and ignored.