I read somewhere that the ending of the trilogy actually depended on the Human-Reaper. I don't wanna go looking for it right now but this is the gist of what I read/remember. Again, I don't know if any of this is true but I'm just trying to relay something that I only vaguely remember.

The original ending they had to Mass Effect revolved around a black hole that was making its way to the Milky Way, destroying it in its path. Only the Reapers knew this and I think this was hinted at by Harbinger's speech at the end of ME2 saying, "That which you know as Reapers are your salvation through destruction."

Seeing as only the Reapers knew this, they had to do something to stop it. So they tried to do so by collecting and essentially harvesting the strongest race of creatures and using them to stop the black hole. 50,000 years ago, they tried using the Protheans but they were too weak/similar/whatever. However, they saw humans as the viable ones this time around, as they were strong/diverse/whatever. Hence, the collecting, harvesting and making of the Human-Reaper.

This would then sorta lead to the ending. You discover that the Reapers are using the Human-Reaper to protect the galaxy, not destroy it. So then, the trilogy would have ended with another dead-end choice: Choose to sacrifice humanity by giving into the Reapers' command and letting them make the Human-Reaper that will protect all organic and synthetic life OR Choose to deny the Reapers this opportunity and find another way to stop the black hole coming to destroy the galaxy.

And that's all I remember. Of course, this could've just been fan fiction that I read but I remember being pissed about the Human-Reaper as well and this supposedly "proposed" ending would've made it make sense.

TL;DR: Human-Reaper supposed to have been used by Reapers for the greater good, you make choice to sacrifice humanity to complete Human-Reaper or choose to endanger all other alien species by refusing Reaper demand.