Indoctrination theory also makes no sense, and also just shoots the series in the back of the head in the best of interpretations.
What really makes sense is the original dark energy plot, which was referenced as far back as ME1 and also makes the title of the series relevant.
You can't just mention a theory I've never heard of and then not explain it like that!
Essentially, people so desperate to avoid the ending of ME3 that "it was just a (indoctrination) dream" and didn't happen. The less bullshit version of it is that the ending is really happening, but Shepard has been indoctrinated and all options but Destroy actually lead to the victory of the Reapers.
No, I've heard about the indoctrination theory. It is the dark energy plot I haven't heard about.
Essentially, the original overarching plot of ME before Bioware's acquisition by EA and the wholesale destruction of the development team had to do with a severe buildup of dark energy caused by the use of the mass effect.
The early mentions of this were in one of ME1's sidequests and the Haestrom mission in ME2. Haestrom shows the seriousness of it, as the planet's star has entered a dying phase billions of years early. That an early quarian colony is in the same system is no coincidence. When element zero is placed under an electric charge, you of course get the proportional reduction of mass that constitutes the mass effect. However, what everyone doesn't know is that this process also creates massive amounts of mostly-unnoticeable dark energy, which in abundance disrupts stellar fusion.
This is the true reason for the Reaper invasion. Eons ago, some ancestor race (would eventually be retooled as the Leviathans) figured out that this was happening. No stellar society would be willing to give it all up, but refusing to do so would ensure the destruction of not just their own society but the entire galaxy permanently. So, the Relays were constructed to efficiently funnel all intelligent life along a certain pathway of mass effect development and a literal pathway towards the Citadel, which for most cycles ended up a natural center of galactic governance as well. The Reapers would arrive every 50,000 years and be easily able to track down all civilizations that had uncovered the mass effect so that they could be processed into more Reapers. Part genocide, part archiving, and part immortality, but in the end it would mean that no civilization capable of using element zero could grow to such heights that it would set off an unstoppable cascade of star death. The Reapers, for their part, spent most of their time powered down outside the galactic rim. In the thousands of years in-between harvests, the dark energy content of the galaxy would be able to fall. An elegant solution to a universal problem, or as Sovereign put it "creating order from the chaos of organic evolution". The Reapers are not capricious murderers, but truly are our salvation through destruction.
How's that for a cosmic moral dilemma? Certainly better than "synthetics and organics fight all the time ikd". Not only is it just a better plot overall, but it does introduce the very clear consequence that even if Shepard does defeat the Reapers somehow, it will only result in the inevitable downfall of the current and all future civilizations through mass stellar acceleration. An act of truly supreme selfishness.
I believe there were some points about how the Crucible's original purpose was to be a giant eezo battery that could kick off the collapse immediately if used, and thus a meaningful threat to bargain against the Reapers with, but that's about the whole of it as far as the abandoned plot goes. It doesn't fully fix ME's problems, like the absurdity of ME2's entire plot being where it is, but it's a hell of a lot better than what we got.