If you subscribe to the Indoctrination Theory, then all the endings except "destroy" are entirely false. You end up indoctrinated and help the Reapers (over the next century according to Liara) finish everyone off over your remaining life-span (just as Saren or the Illusive man did.) Given that a high EMS and the "Destroy" option gives a scene of Sheperd, still on earth, presumably near the beacon, the other endings seem impossible. "Destroy" does not magically teleport Sheperd to the base of the beam, even in the extended cuts, which I view as a mistake. (If IT is true, the others are false and all the extended versions did was further confuse the issue by attempting to clear up seemingly impossible endings.) Thus you never made it to the Citadel/Crucible at all. The possibilities seem mutually exclusive to me.
I think there are 2 problems. 1- Bioware expected too much from their audience with this ending. There is far too much to figure out, and much of it requires you to remember events/dialog that took place in ME1 (the Rachni conversation.) This isn't just a set of 3 novels. You are talking about hundreds of hours spaced over 5 years of time. I picked up on a lot of the clues, but not all of them and was left fairly confused. After watching what people have put together in the videos about IT, it all falls together. If the ending you wrote requires hardcore players to watch a video created by other hardcore players to understand, then you have gone too far. It is one thing to do this with a movie/ book like Inception or BladeRunner/ Do Androids... Doing it with a video game with hundreds of hours of content is too much.
I had an idea about 2 years ago. I wanted to write a video game story whereby I took advantage of the natural limitations of video game tech and the bad writing that has been such a part of many games for so long. Basically what people mistook for being the usual tropes of video games would actually be me hitting you in that face over and over with the reality of the situation, but one you would dismiss as being poor writing or the tech limitations/ staples of video games. Having seen what kind of reaction that approach has provoked with ME3, I'm glad I never got around to doing much of anything with it. They did hit you in face with it over and over in this game, and to a lesser extent in previous games, and look at the reaction.
Problem 2. The EA buyout, DA2 and TOR. Bioware lost their trust with a lot fans thanks to DA2 and TOR. Being owned by EA just upped the suspicion another notch. People are more than ready to believe the worst. How many just looked at the ending and went away angry? Didn't take a second look, or think things through with a trust that Bioware knew what they were doing? They just assumed this was more of Bioware falling apart, abandoning their core fans (the action centric/ loot removal in ME2 didn't help this at all), blaming EA for cutting budget (obviously the game isn't finished and was forced out by those evil publishers - we'll probably get a true ending as pay DLC), etc, etc. The endings were just flat out impossible, and instead of going through it and figuring it out, people reacted angrily and stomped off.
So basically, Mr. Catalyst rebelled. 
