To be honest, I just think that the Mass Effect 3 endings... Didn't fit into the lore, at least not for me. The whole god child AI / energy being creating the Reapers as a way to keep the Synthetics from destroying the organics forever, and instead only annihilating the advanced ones capable of creating the AIs just made me grind my teeth. Even though it made sense, that doesn't mean it's a whole lot more plausible and acceptable than that of an entire ancient species rather than a deity-like being creating the Reapers, and through an accidental conception of their sentience, in the stead of purposeful design by said 'god'.
Not to mention the Indoctrination Theory has a lot more subtlety to detail and the supposed hints and signs that only the player can recognize as indoctrination would have been a mind blowing troll on people playing through that end sequence, only to find out that the whole thing was a 'dream' intended to acquire Shepard's mind, and that choosing Synthesis or Control as an ending ends up with you waking up indoctrinated and under Reaper control, killing your allies and bringing Earth to its knees... And ultimately destroying all that he had worked so hard to achieve because of players failing to notice the signs that Shepard was being bombarded by attempts to indoctrinate him.
I also don't like the fact that choosing the new 4th ending means you lose no matter what, and that hoping the battle assets you built up would be enough to at its least, stop the Reaper threat from destroying the galaxy, if not Earth... Also were useless.
Long story short, I would like the effects of all the choices you made throughout the game and the trilogy as a whole effect whether or not you can destroy the Reapers, not that the last choice is up to Shepard, but that all of the past choices he has made will effect the overall resolution as well as the minute details. It should have shown that Shepard is just a man, and that he alone cannot decide the fate of the galaxy, that his mustering of the galaxy and uniting its occupants to the point where it is enough to combat that threat, because it shouldn't be up to Shepard choosing the way the Crucible is used to decide how he wins, but that the only way he can win is with others, and A LOT of others.
Also, I disliked that they made the Reapers... 'Humanized' in the sense that committing genocide on them through the Destroy ending would be a lesser alternative than Control or Synthesis, even if they did that exact thing for countless cycles and coupled with the way they indoctrinate people, just goes to show how willing they are to convince and lie to the minds of the organic beings that there is another choice than fighting with them, and that looking for a peaceful solution is possible all the while they slaughter all of them indiscriminately.
As an example of their trickery, Sovereign indoctrinated Saren by making him believe that he can do the equivalent of the Synthesis choice, which is combining organics and synthetics into a new cyborg-like species. Which was a complete lie used to manipulate his political stance as a Spectre, above the law, to wreak havoc on the organics even before the Reapers come back from dark space.
Basically all I wanted is the Reapers to have remained an ultimate evil, and the peaceful coexistence they were offering is just a ruse meant to fool people into believing them, and then become indoctrinated.
... Bioware, I am disappointed that you could not have made the ending better.
