The reapers operate on a certain theory about how history will play out. But they can't really let history play out further than their own first cycle, because if they do that, they run the risk of not being able to carry out their preservation order. This limits them to always the same facts and arguments making up their theory, without getting new input to probably alter it.
So assuming history repeats itself along similar lines at similar civilizational and technological tresholds, they will never gain new input resulting from unexpected developments further on. For example, the Romans couldn't envision certain technological and cultural advancements we have today and ths could not have anticipated how international relations today look. humanity could develop into something we today could not foresee because we miss a possible development that is happening somewhere in the future.
The catalyst and synthesis is in its essence such a development: over many cycles the races have produced a technological advancement going behind the point the reapers hit the reset button , and subsequently the theory has to be altered.
The problem is the game just does a bad job portraying these things to the player in general. the synthetics vs. organics inevitability could've been so much better done as i said earlier, but even if the storytelling was very good in mass effect, the required depth for such a topic was just missing.
perhaps another, crude example: It's like if you killed off humanity at the end of world war II, after the nuclear bombings, throwing it back to te stone ages, and subsequently would kill it of again and again when it reaches this point in history, because if you let them evolve past that point, you could lose your superiority and ability to kill them off before they extinct themselves. But then you let them evolve past this point and suddenly you see they do not necessarily eradicate themselves but could even have the potential to spread to other celestial objects, thus minimizing the chance of extinction. (but could possibly still do it in the future)