I think I may know why the Reapers harvest organic life every 50,000 years.
Here's the excerpt from Mass Effect: Retribution, Chapter 26, Pages 324-326:
Kahlee was trying to think of a way to reach Grayson. When she'd tried to appeal to him directly, the Reapers had shut him down. But when she'd asked the Reapers to go slower, Grayson had been able to exert some kind of subtle influence over them. It almost seem as if making the Reapers focus on something external loosened their hold on Grayson, allowing him some limited type of freedom.
"Why are you here?" Kahlee asked. "What do you want from us?"
She wasn't sure if the Reapers would even reply. All she was hoping for was that she might be able to engage the Reapers enough to give Grayson a fighting chance. A fighting chance to do what, however, she couldn't say.
"We seek salvation," Grayson said, much to her surprise. "Ours and yours."
"Salvation? Is that what the Collectors were doing? Saving those human colonists? Is that what you did to Grayson?"
"He has been re-purposed. He has evolved into something greater than a random assortment of cells and organic refuse."
"That randomness is what made him unique." Kahlee countered. "It made him special."
She noticed that their pace had become more measured and deliberate. If Grayson was still inside there, if he had any influence at all, he was using it to slow the Reapers down. He was trying to buy her time to escape. The best thing she could do was try to keep them talking.
"We are the keepers of the cycle. The creators and the destroyers. Your existence is a flicker, a spark. We can extinguish it - or we can preserve it. Submit to us and we can make you immortal."
"I don't want to be immortal," she said. "I just want to be me."
They were barely moving at all now. Grayson had managed to bring their hurried escape from the Academy down to a crawl.
"Organic life lives, dies, and is forgotten. You cannot fully comprehend anything beyond this. Yet there is a realm of existence beyond your understanding."
There was something odd about the things Grayson was saying. She knew he was speaking on behalf of the Reapers, but it seemed like he - or they - actually wanted her to understand their position. It was like they were trying to persuade her to agree with them, but they didn't know how to frame their arguments into anything she could relate to. Or maybe there was simply no way for organic beings to relate to hyper-intelligent machines.
"We are the pinnacle of evolution," they continued. "Yet we see potential in your species. You can be elevated. The weakness of organic flesh can be cast aside. You can transcend yourselves."
The words didn't make any kind of compelling argument, but she felt as if there was some deeper meaning to them.
"Your understanding is limited by genetics. You cannot see beyond the brief instant of your own existence. Yet our knowledge is infinite, as are we."
The more Grayson spoke, the more his words made sense on a deep, almost subconscious level.
"The laws of this universe is inviolate. Immutable. Your resistance will only lead to your extinction. What are - what we do - is inevitable."
Kahlee was so far under the Reapers' spell, she wasn't even aware she was nodding along in agreement.
So it would seem that the Reapers subtly indoctrinated her into trying to understand and agree with what they're saying. But that isn't the point. The point is why do they repeat the cycle and continue on their merry way? The Reapers give valuable insight into themselves, calling themselves the "creators and the destroyers", and the "keepers of the cycle" - possibly meaning that they think it's their duty or destiny to carry out galactic extinction every 50,000 years in order for another race to reach its apex and start the cycle again. It also shows how they think that organics are inferior, and that they see humanity as a possible/better pawn than the other races. What do you guys think?