Another aspect of the ending people don't like, or rather hate, is that there was no choice, that we had no control over the situation. From reading reactions and posts from people who liked the given endings, like myself, they make a clear distinction between choice and control (and not the control ending, just to be clear).
I never got that distinction, at least on a conscious level, because I went perfect throughout all three games. I never missed a side quests, a loyalty missed, or lost anyone other than Mordin (because I was honest to a Krogan Female who respected me as a friend. How could I betray her and her people like the Salarian's wanted me to do?) and Thane. Mordin's death I could have controlled but with consequences. Thane's death I couldn't: it was beyond my control. As were the events on Thessia, which I raged about before, and even talked to my therapist about (apparently this game is great therapy material), but it never clicked with me that even if I may make choices, and that they matter, sometimes I will have no control over what may happen.
I had no control over the end. I had made my decisions, I had planned my attack, and at the end, I had no control over what happened over than making one of three choices.
My mother, among countless others, constantly remind me we have no control in life; just the illusion of control. We may control our thoughts and behaviors, the guiding forces behind what makes us who we are and what we do in life, but we cannot control our emotions. And, sometimes, the choices we make in the past make things impossible in the future. That is real life and that was personified in the game.
Let's take an easy example: a family member dies. In my life, I had the honor, and horrifying, experience of watching my grandfather die in the VA hospital. I had no control over what happened, whether he lived or died, and all I had were my choices in my life, of what I told him, of how I didn't email him enough, of how I did this or that or not enough. I could not control what happened to him, but die he did (RIP Grandpa), and my choices before that moment were what defined my relationship with him.
It's as the old AA saying/Serenity Prayer goes, something I believe everyone should know by heart:
God grant me the serenity to accept the things I cannot change
Courage to change the things I can
And the wisdom to know the difference
Did Shepard have a choice going into the final battle? She sure as hell did and she rallied every species she could as much as she could. But when it came down to the wire, when all was said and done, when all her plans came to fruition, did she have a choice? Did she have control? Even without the indoctrination theory would she have had control over events that she couldn't change, ie the Crucibal firing, the ground troops, the relays.
It's weird, the illusion of control in our lives, but the things we do control are ourselves and how we react to certain things. Sometimes things happen and we can't control them. We only need to know when we can change what can be changed and not fight what can't be.
Did that make sense? Probably not, but I think it's an important point that isn't said enough. Maybe Shepard had no choice in the end. She had choices before and she made them, for good or for ill, except was there control in the end? Do we ever control our own demise, our own legacy, or even our own fate? Could Shepard?
BioWare made us a promise of choices. We got them and they affected all who played deeply. They did not, however, make us a promise of control. Let us hope we know the difference.
Ok, time for bed. I hope I can sleep tonight.