I've watched several good videos about that theory that has been running around the internet with Mass Effect 3's endings. I heard Bioware's appeals to their fans, I felt something strangely familiar.
Then it hit me.
I was saying the same things several years ago when I launched my first game
My game was built around NPCs trying to deceive not just the character you play as but you as a player.
What I noticed was that players were thinking that a lie made by a character was "the truth" and just bad writing. I had intended the lie to be a poorly-thought out lie so that players can recognize it as a lie. Therefore they would find the liar untrustworthy. But they just believed it and thought it was bad writing. And you can see this in a few of the reviews of the game.
Mass Effect 3 had the same thing happen on a far larger scale. People thought a lie was just "bad writing." It's one of the various practical problems of having choices in an interactive storylines. (as opposed to the overabundance of theoretical issues in making interactive stories in video games)
Conspiracy Theories? Had those too!
It was really interesting to see the arguments over the different forums as I was also the target of "conspiracy theories" when I received good review scores. Some people were wondering "Why did this game get such a good review?" Of course once they were in on the secret they seemed to suddenly go silent. Oh... it definitively looks like something bad is happening to whoever speaks up loudly and then goes unnaturally quiet. Maybe I'm paying them off? I hardly have the money to pay off that many people anyways. If you heard my story about getting to Anime Expo in LA...
How to Avoid the Negative Backlash?
That's the trick isn't it? While good publicity for their game, it's actually quite a handful to deal with and you have to survive long enough for enough people to figure out the truth. Undoubtedly for Bioware "handful" is an understatement.
One way is to throw the peers of the protesters at the protesters by letting a few of them know. They definitely tend to soften the blow. However, since no DLC isn't out yet there's no way to know for sure. For myself, it was simply a matter of speaking few spoilers to stop them from going too far. Those still under the illusion are a handful and those who broke your illusion are your best allies.
Second way? You absolutely need to make sure you teach (or burn) the player with your trickery by about mid-to-late game so that they understand that you can pull this stuff off. They MUST understand that they were fooled and you gave them enough of a chance to figure it out themselves.
What does this all mean?
That theory that is flying around about the Mass Effect 3 endings? Based purely on Bioware's reaction to the uprising (i.e. Retake Mass Effect) and how it compares to my experience releasing a game with free will and player choices like Bioware's, it seems there is another piece of evidence is added to large pile supporting to the theory.
I'm throwing my chips on this theory and declaring it true. I'm calling before they reveal the DLC!