That wasn't really weird though. Sovereign explained in the first game they only harvest civilizations that are advanced, IE space travel, etc....and all this other extra shyt wasn't planned until late in the 3rd game. So they had 2+ games to come up with a better reason why the Reapers exist.
That's why Synthesis doesn't fit. If they had it planned since the first game, they could've dropped clues....but it wasn't planned, that's why the first two games you fight people (Saren and The Illusive Man) that want to "control" or "join" (synthesis) the Reapers. If we're going by what makes sense in the context of the series, Destroy should be the only "correct" choice.
Fred.
Destroy is the "correct" choice in the short-term. In the long-run organics would create new synthetics like the reapers that would threaten their existence and the cycle would continue again. Synthesis is the answer to ending the cycle.
The clue from the beginning was that the Reapers did not wipe out all traces of organic life in one fell swoop - which they were more than capable of doing. They left less advance civilizations intact which lead me to believe that they weren't completely mindless killing machines - that there was some rationale behind their actions. A rationale we didn't understand until speaking with the ghost kid.