It all makes sense logically to me.
I really hope they've got some really amazing twist like IDT or the Manipulation Theory coming for us.

Ballsy, but brilliant IMHO. I honestly do not believe that the writers would fudge up this badly considering the scope of the story. They're very, very detail oriented people. Patrick Weekes recently spoke on his twitter about the existence of a style manual for writing which delineates capitalization of words, hyphenation, etc. I guess people are pessimistic about Bioware with the DA2 ending (have not finished yet, so I can't comment further...), but that game was written by a different group of writers, anyhow. It's just, the entire story has been so well written, with such a fantastic and intricate universe... and the ending, so I've heard, was hashed out in the very beginning. They even have that one planet in ME1 that talks about the beings of light. I think there's more to all of this, here, than what meets the eye. And as it has been stated, devs have pointed out to not necessarily take everything for face value.
Also, the Reapers believe they're unstoppable because they've been doing this for countless cycles. They would not fathom that one person out of one race (out of potentially millions of races) could destroy them. In addition to this, wasn't Soverign the one to say we could not possibly comprehend the purpose of their existence? I think it was presented to us in an understandable (although contradictory) manner that they are killing organics to save organics from creating synthetics which will eventually destroy organics... so anything they do must have a deeper meaning to it, like making Shepard indoctrinated or manipulating her...
I feel like I'm rambling and I hope that all kind of made sense because I am half asleep here.
There's
no way they derped the ending when they spent the last 8 years leading up to that point. It may not be the indoctrination theory, it may not be manipulation, but there's something.