Well, the crucible and the three choices (however dumb that may be) has nothing to do with the reapers plans, so it doesn't really have any bearing on their motivations or criteria for "ascension" to reaper form.
Initially I did actually wonder if the crucible plans were introduced into the cycles by the crucible itself. The EC (I think?) put paid to that idea since you can ask directly who came up with it and the response was a disappointing "you do not know them, and it would take too long to explain." That made me think it might be survivors from whatever race created them, so Leviathan looked promising for this theory for a while, but that doesn't appear to be the case either.
I suppose it's good that there are some mysteries. I mean the cycles have been going for at least a billion years, averaging about 50,000 years a go, that's around 20,000 cycles *minimum*. Plenty of time for all kinds of variance in the pattern. Perhaps one race succeeded in a similar initiative that Javik attempted and managed to preserve a substantial population into the following cycle? Maybe a race took a page out of the reaper's playbook; retrofitting their surviving fleets as stasis arcs and sending them out into darkspace where they can't be tracked.
It would be nice to think that the last cycle wasn't *completely* unique and some other race at least gave the reapers a run for their money. Maybe something like that is what actually prompted them to build the relay network and citadel; to increase efficiency and better control the colonization patterns of emerging civilizations.