I have thought long and hard about why this is the case. My first two blog posts do an adequate job explaining the thematic whiplash the last five minutes of the game gives you, and I discuss plenty of the plot holes, but it is not enough. After I finished the second part, drinking a nice cold sweet tea, I still felt empty, still felt there was something left to explain. Now, as I write the THIRD blog post on this annoyingly complex issue, I think I have the answer. Our angry reactions to ME3's ending can be summed up with two statements. Number one, the ending erases and undoes much of the pathos from the previous two games. Secondly, the writers do not reveal to us the truth about the Star Child's "cycle".
Let's take the "control" ending, for example. Throughout the entirety of the game, Shepard and the Illusive man argue whether 'control' is viable, despite the mountainous amounts of evidence saying it isn't. The player is never given the option to ally with the Illusive Man in ME3 or pursue 'control'. Shepard, as a character, as the primary protagonist, and as written by the writers, fully and only endorses 'destroy'. It's confusing and undoes large chunks of the game then to have at the very end 'control' as an ending! In unprovoked dialogue, even Shepard admits, "So, the Illusive Man was right after all."
What if from the beginning of ME2, Shepard endorsed 'control' and supported research to that effect? Even if you engage in the terrible experiments the Illusive Man is shown to be a part of, potentially you're looking at far less loss of life compared to the causalities you suffer against the Reapers through war as shown in ME3. It's not fair to the player to, in a game known for decision-making, force them to fight for and agree with something that turns out to be total BS. I guess you can thank the Bioware writers for telling you what to believe only at the very end to tell you're wrong and stupid for thinking so.
What's so fantastic about Shepard in particular? He is not any special product of evolution as the Reapers destroy all advanced life at given intervals. If he's special because of his will to fight or his virtue, you could argue there are plenty of people who fit that bill. I would recommend Winston Churchill or Mother Theresa to start. If the Reapers were REALLY interested in synthesis is seems like they could've shored up the problem long ago. How many other people or species were "worthy" of synthesis, but couldn't quite get the crucible ready in time? If you start doing the math here, I think you wind up with a rather large number of senseless deaths. The ending, in my opinion, just seems to make a lot of important events in the other games completely redundant.
The second underlying reason why I think we hate ME3's ending can be summed up with the question; Is the Star Child being truthful? I cannot stress enough how vital this question is. At its core it is the founding father of the Indoctrination Theory, and it is at the heart of why 90% of fans, including myself, are so confused by the ending. The problem is that how you answer this question determines which ending you'll pick, but the writers don't provide enough evidence either way. It is impossible for the game to be entirely true and have each ending lead to the same result with only slightly different pros and cons. No, depending on what you believe, choosing a particular ending could save or doom the universe.I chose 'destroy' more or less because I saw little reason to believe anything the Star Child told me, but what if I'm wrong?
One reason I hate 'synthesis', is because the writers highly imply it's the "good" ending but logically from an in-game perspective makes little sense. Who's to say that giant laser running through the Citadel isn't exactly what it appears to be; a white-hot death-ray? Oh right, it's the guy who's up front told you he's been trying to kill every advanced species in the universe for the last three years. And what a coincidence, now he wants you to jump into it? Nothing to be suspicious about here. It's not fair to morally hedge a player in a certain direction yet provide little logical incentive to their character to do it, especially when the stakes are this big.
The reason the Indoctrination Theory took such hold is because the choices and their revealed outcomes as shown by the game don't make sense. As stated previously, 'control' has never been shown to work, so why does it all of a sudden work now? Why does the Star Child only talk to Shepard about synthesis at the end, just when he's close to being defeated? Why is the process so vague and magical-sounding, something that can only be done by Shepard? Yet at the end we see a happy Krogan family with mystical green eyes. No, something's off, and at that moment of time, when we were emotionally fragile and despondent, the Indoctrination Theory became our lifeline, one last working lifeboat on a sinking Titanic.
Ultimately then, we dislike the ending because we want to know what happened to our friends and the outcome of the war with the Reapers, but instead we get a pointless bundle of nonsense that only leads to many more questions about the reality of the Mass Effect world. That's frustrating. It's agonizing. And it's doesn't seem fair. How to best solve this problem then, is up to the player whether that be somehow making the endings work best at face value in your head, the Indoctrination Theory, a mod, or maybe even making up your own head canon. I can't solve this problem for you, but perhaps together we can finally resolve our pent up feelings over the ending of Mass Effect.