Okay, my theory.
Reapers creators, known as 'The Masters' for the purpose of this thread, either set up the Relay system and Citadel station as their own, or all this was the Reapers creation. One or the other, I'm unsure. I swing more toward the former, as the technology does not resemble the Reapers.
I see the Reapers creators being much like the Reapers themselves, considering themselves the peak of evolution... most advanced, and with quite a (sadly well earned) attitude about them. They create their ships in their own image, like Gods would. Their ships link up with them, and much like the Geth, the Reapers begin to second guess their creators... only since they were made with such advanced tech that they would be part of their creators minds (mentally controlled, perhaps, instead of cockpits and buttons and such?) they start to adopt their creators ways of thinking... and see themselves as the rightful Gods.
They wipe their creators out. The fact that Reapers can link with, and dominate the mind of sentient organics, and need them as a resource leads me to think that they were always created with their Masters integration in mind. They simply take the innitiative. Now that they are in control, it doesn't change the fact they NEED to fulfill their original requirments to function... their Masters. They need the organics. And so, whether they repurposed the Relays, or created them, the Cycle was created to ensure that they would get what they needed.
I don't believe there was ever an instance where this Cycle was broken... therefore, never an instance where they needed to fashion a new one of their kind, from the hands and material of anything but their old Masters. The fact that Collectors built the Hybrid, but it was fashioned from human material, and ended up resembling the humans instead of Collectors leads me to think that they've never had to really lay down the procedure before. Yes, they look like their creators... they were made by them, and are made of them, at the same time, their fusion born of their Masters God like opinions of themselves, and their need for seemless integration.
But now, a Reaper is built by one species, from the materials of another... this is new, a variable they haven't considered. They likely chose Human over Collector for psychological reasons, as humans are an enemy to them, and have pretty much gained their attentions by now with destroying Soveriegn.
So, I do believe that The Masters resemble their creations, the Reapers, but what were they? Lets see... most popular belief is a squid like species (obvious reasons) but I don't believe this. Here are my points that have lead me to my conclusion... please note each carefully, as they will come together afterwards.
1. The Reapers were created to be gentically similar to The Masters, as hinted at by the Reapers need for organic life as a resource, their fashion of construction as seen in the Hybrid's creation, and their mental affinity.
2. The Protheans, an organic species, likely mammal and definitely bipedal, end up as Collectors after their Indoctrination and repurposing. They end up as an insect race... why?
3. Harbinger, a Reaper, can take command of Collectors at any time, yet it is far away, possibly in Dark Space, which is why they need the Hybrid. If Soverign could not contact his fellows so far away, yet his fellows can contact the Collectors, then was Soverign a victim of his pride, much like his Masters? Or were they designed with a different method of communication?
4. The Hanaar were created by the Protheans. This is my weakest point, more of a hunch, but the Protheans were very interested in the Citadels origins... they pursued them enough to reverse engineer the Relays, and figure out the Keepers ultimate purpose. Who's to say that, in their blind fumbling for answers, the Hanaar weren't created as a partial step towards answering the identity of the Masters?
5. The Rachni were sent crazy by Indoctrination... Indoctrination only works in close proximity, over a period of time. A passing Reaper managed to confuse and corrupt an entire sentient race of telepathic insects, resulting in their confused and rabid conquests. What was different? Why was a Reapers mental affinity so strongely recieved?
6. Remembering that the Protheans built Ilos in much the same manner as other races (Humans, Asari) after their repurposing, they adapt and add to their ships much like termites, building with their own organic material, much like The Masters built the Reapers with their own organic materials, in some sense or magnitude. Once again, why? Why change the Prothean's so? Was their insectoid ways and their genetic makeup more then just essential for the Hybrids creation? Or was it FAMILIAR?
All these points, with the possible exception of point 4 lead me to one conclusion...
The Masters were insectoids.
Think about it. The Reapers can connect so easily with the Collectors, even at such a distance, and when they cannot connect with each other as strongely. The Collectors were fashioned from the Protheans, changed from what they were, into insects, as The Reapers know the Masters genetics best. The Rachni reacted so strongly to them.
My theory is that The Masters created Reapers to be similar in gentics and mind, and therefore, the Reapers could not exist without them, therefore, the purpose behind their Genocide Cycle. They need the organics after conquering their Masters. They created Collectors, to use their Masters mental affinity. The Collectors bargain for the odd things they do for Reaper purposes. The Rachni were unfortunately too compatible with the Master/Reaper link, and so were driven crazy.
My theory towards the Reapers origins and motives... hope it made sense.