Leaving aside the rhetoric -- comets, really? -- this isn't a particularly hard problem. Humans had unmanned FTL drones during the FCW. How much better would the Reapers be at building them? Sure, you need them by the thousands to check everyplace in a reasonable number of centuries, but you've got time. Hell, the Reapers should have the tech for von Neumann probes, which would be free.
"Taste like bacon" and procreation only work if the Reapers are flat-out stupid; the harvests are horribly inefficient as a method of production. Malfunction can work, since that's irrational by definition. I don't see how that's any better than what we got, though.
The volume of the milkyway is 8 trillion cubic lightyears. A cubic light year is 10^39 = 1,000,000,000,000,000,000,000,000,000,000,000,000,00 cubic kilometers... Now multiply that by 8 trillion.
Yes, you can technically built a trillion von Neuman probes, which will then use a giant amount of ressources and energy, which would have then been available for organics to develop. That would be stupid and probably more wastefull in organic life, than a god ai wiping all life out one more time and then leaving.
Taste of bacon and procreation works fine, on the assumption that they want sentient organic life. They are machines and can limit their own growth stretching the finite ressource of sentient organic life as long as possible. If you kill all your pigs for bacon, then you won't have any new pigs, ever... Think of it, as enviromentally friendly hunting, you just cull the herd, here and there.
There is no need for the wastefull expenditure of checking every square inch of the galaxy/universe.
Malfunctioning is better too...
Because what we got is... like going to a doctor: "Help I can't walk... My ankle must be twisted or broken even." Doctor: "Here's a bandaid and drink plenty of water for your split personality." You: "That... makes no sense, do you think I'm stupid?" Atleast baconsentients, procreation or malfunctioning, would be like twisted or broken angle. Plausible...
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Anyways... all of this have been explained, discussed, shouted and what not, over too many pages to rehash here, but I can sum up my universally applicable expectations/wants to "endings" (in general):
I prefer them with some bad assery, if the content thusfar contained action.
I prefer them to make sense. Unless containing "crazy" in which case, anything the mind can think off goes.
I prefer them to actually finish the story. If I wanted to make up my own story, I would have. I wouldn't have bought your book, game, movie to specifically have you tell me a story of your making. Dont skimp out on your damn job.
I prefer "simple"... Quantum mechanics are complicated and makes for a poor story. Evoking basic human feelings like love, anger, jealousy, pride, sorrow and so forth... isn't complicated. We all have them (most) and it should be easy to speak to... Stories don't necessarily need to contain the meaning of life or ... quantum mechanical mindblownness... Evoke the emotions and you have a good story.
It doesn't have to be a happy ending. It can be dark or grey, but for all I expect a good ending to emotionally engaging. Either leaving you elated, sad as hell or both at the same time. If you feel numb or disinterested... it wasn't a good ending.
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That's MY taste... It doesn't have to apply to you girls and guys.
How much is applicaple to ME: Andromeda only time can tell... but I look forward to more spacestuffs!