I think that the big problem is... they tried to give us all this reasoning and logic and origin and history behind the Reapers... and honestly, I don't think any of us really WANTED that. I mean, when we first met Nazara (Sovereign) in Mass Effect 1, he said to us, rather honestly, a few things about the Reapers.
1: We're going to kill you all. Nothing you can do to change our minds, nothing you can do to stop us.
2: You can't EVER even begin to understand us. Don't bother trying.
3: We're not at war with you all, just like how you're not "at war" with ants that you crush while you walk. You're completely below our notice.
4: And by the way, we are RIDICULOUSLY old, and we've done this literally thousands of times, if not millions of times, before. You're not special, it's happening again, die quietly.
And that's what makes a good Force of Horror. That's what the Reapers really ARE: Unknowable forces of horror. The Heretic Geth, who are LITERAL Killing Machines, worship them. They look like squid (which scare the shit out of me) and/or giant hands, as if metal deities are reaching out to choke the life from you. Why they felt the need to explain and rationalize them AT ALL, let alone making them the Universe's most annoying VCR, that not only blinks 12:00 over and over, but also kills everyone everywhere when it does, is beyond me. It's ludicrous.
All of the STORY that people really cared about was between the, for lack of a better word, mortal races of the universe. It was about all these different people and machines and... jellyfish, coming together, despite their differences, to stand against inevitability. For the first 299 hours and 45 minutes, the Mass Effect Series' big message was "We don't all have to be the same, because our differences give us unique contributions. We can all be free, and we can stand together even when we disagree on some of the most fundamental issues of being alive in the world. And that was GREAT.
Then the last 15 minutes said, "Nah, being different is wrong, we should all be the same, everyone needs to conform or die, give up what makes you YOU, become just another copy of ME, and also, SPACE WHITE POWER!!!!"
Wow. What a waste. What a squandered opportunity to be a major literary triumph that championed individualism, self determination, and equality. Instead, they tried to pole vault into high-brain Techno-human-synthesis, missed the bar, flew through Mrs. Johnson's kitchen window, landed on her stove as she was making breakfast, and then, shrieking in pain from the hot bacon grease on its face, Mass Effect 3 Ending pooped itself, and ran home crying.
Way to go. SO glad you didn't just give people something hopeful and rewarding.