I don't necessarily agree with it, but I've thought a lot about what the writers tried to get across with synthesis.
I feel that your conversation with Vendetta is crucial to understanding the writers' attempt to tie it all together, so I'll start there. Vendetta describes the evolution of life as a cyclical pattern that always reaches a peak and subsequently resets itself. That peak is the conflict between organics and synthetics, a conflict that has appeared under many different contexts and circumstances, but one that ultimately ends with intelligent life being blasted back into the stone age at the end of each cycle.
Now this is the crucial bit: Vendetta reveals that the Reapers actually serve this pattern and are not its masters.
This leads to my understanding of the situation, which is as follows: each side of this conflict is correct in that they recognize that this peak in the evolution of life is a problem that needs to be solved since life can not evolve past it. But there is something wrong with the way each faction chooses to go about solving this problem.
The Reapers try to manage this problem through control; by leaving their technology for civilizations to use, they control the course of evolution so that they know when to intervene before civilization advances too far, and in their view, preserve life before it destroys itself. But appart from being repulsive, the Reaper's solution is actually in service of the pattern, as life reaches its peak, it's blasted back to the stone age.
The goal of Shepard's faction is to simply eliminate the opposition, which would hopefully allow life to move past the peak. As it happens, though, the only way to eliminate something as powerful as the Reapers is to eliminate everything else like them, which creates a problem with this solution as well. The cost of destroying the opposition is the destruction of all synthetic life and most of the technology that life relies on, effectively blasting life back into the stone age, making this solution in service to the pattern as well.
So synthesis, it would seem, is designed to solve this problem permanently, giving each form of life the abilities it needs to prevent the entropy that leads to the evolutionary peak, effectively eliminating the cycle.
Now personally, I don't believe that this should be the only way to move past the peak; ideally, there should be a way to destroy the Reapers while preserving the cooperative synthetics in the galaxy. As it stands, this just isn't possible.