The things you reference display use in an ecosystem within which you're an active participant, whereas the Reapers stay away until action's required and return to darkspace after they're done for the next step in their agenda. [...]
The Reapers display no use for galactic life and its resources, only imposing order over their chaos and growing their numbers to aid in their dominance. Your position only makes sense if organic life serves a tactile purpose for them, and beyond reproduction and cultivation in ME2 and ME3 that's more about preserving the continuity of genetic material and paying tribute, there's never any indication whatsoever that the Reapers have any use for anything produced by the dispersal and advancement of civilizations. They're vermin, bacteria, things with which you call exterminators and pest control to take care of ... and you don't wait until they're at the apex of their glory before doing so.
They're called Reapers and they harvest : of course they have a use for galactic life. It's reproduction, which you dismiss as if it doesn't matter at all. It's reason enough. By harvesting entire galactic civilisations, they can create another "perfect" being, another Reaper. How is that not a good reason? Just because those civilisations are "bacteria" doesn't mean that the Reapers should exterminate them for no reasons. It's another gratuitous conclusion. The human species needs some form of bacteria to survive : they shouldn't be exterminated on sight. The Reapers need them ("us") to reproduce : if that's a goal, they shouldn't absolutely annihilate them, but rather destroy them in the form of a harvest they can use.
You can, but it doesn't make any sense when applied to mecha-Cthulhu who are the pinnacle of evolution and the end of everything. [...] There's no reason for them to stall the annihilation of organic pests they're absolutely going to annihilate, unless there's an agenda imposed that tells the annihilators to wait until some other time.
Cthulhu's ambition is to rule the world, even though humans are nothing before him ; hardly a good comparison. And again, you assume that if the Reapers really thought that galactic civilisations were nothing more than bacteria, they would absolutely annihilate them. This would need a better justification. As for why they stall not the absolute annihilation, but the harvest, it's because they, themselves, are made of the genetic material and cultures of those civilisations. Waiting for them to reach their apex makes sense.
Read those quotes again, and think about words like "extinction" and "annihilation". That's the attitude being projected by the Reapers; whether it's the truth in terms of the agenda they service is something else altogether.
Those quotes only mean complete and absolute annihilation when considered abstractly. In the context of the games and the harvest, it means something else completely, and ME2's ending made it absolutely clear what it was : destroying civilisations, for the Reapers, means using them to create Reapers then wiping everything out in order to leave no trace. That's all you need in terms of agenda.
If they're so beyond it and it's nothing but a nuisance whose extinction is "inevitable", they have zero reason to continue to let it thrive. Reapers have no need for reproduction, especially if they are so contemptuous of the material that goes into the creation of each one.
That's the most gratuitous thing you've said yet. Why wouldn't they want to reproduce? And why wouldn't they do it if they had contempt for the material? A lot of people have contempt for the animals they eat and don't care at all about their treatment ; yet they still eat them. Some feel the same about sexual intercourses too ; yet they still do it in the name of reproduction. Again, you draw conclusions from premises that don't suggest them in the slightest.
If one cycle were able to do that, other cycles were able to do that, and it would be entirely avoidable by coming in sooner instead of later.
The citadel's signal, I said. The Reapers usually start their harvest with a surprise attack on the citadel, which makes the rest much easier. This cycle, it didn't happen, which made the resistance much stronger.
Why would they preserve the cultures and memories of vermin, bacteria, and nuisances if it weren't in service of a higher order?
It is in the service of a higher order : themselves. They're made of the stuff. It's the only reason (and you keep ignoring it) they don't come sooner.