Agreed.
Actually we know for a fact that the extinction cycles don't occur exactly 50,000 years apart. The Inusannon were the species to be annihilated just before the Protheans, and they were wiped out 127,000 years before Eden Prime. That means 77,000 years passed between the Inusannon and Prothean extinctions.
Yes, but we also know that the Reapers hibernate between cycles. It makes more sense for a cycle to begin later, than to begin earlier. If they didn't wipe out the Vorcha, Yahg, and Raloi the next cycle would probably begin in 2,000 years.
There are also curious indications from the planet descriptions that may have blasted even bronze aged species to oblivion...
...I am skeptical of that, though. That planet, Aphras, is in the same system as Tosal Nym which only had primitive oceanic life. Tosal Nym was also hit from space. That isn't the Reaper's MO. Both planets are in the same system as Zada Ban, which had evidence of Prothean mining infrastructure. And both extinction events occurred during the Prothean cycle.
All of that, taken together, suggests it was actually the Protheans that may have caused the mass extinction on both worlds. Why? Perhaps they viewed it as mercy- oblivion being preferable to submission to the Reapers. Who knows.