I like Indoctrination Theory. It's a nice way to interpret a poorly-written ending. Making lemonade and all that.
But would bet money that Bioware never intended it. I have two primary reasons:
1. In Mass Effect, a single wrong choice never causes you to lose.
Indoctrination Theory relies on the belief that Synthesis and Control are, in essence, flashy Game Over screens. Shepard fails to fight the indoctrination and ends up a slave to the Reapers. This goes against one of the basic premises of choices in the Mass Effect series: all the options the player is presented are valid. Saving the Rachni doesn't cause them to ravage the galaxy down the line. Siding with the Geth doesn't backfire. No single choice made by the player dooms Shepard or the galaxy. You could argue that failing the Suicide Mission in ME2 is the result of choice, but that involves such a large collection of omissions and failures along the path of the game that you practically have to go out of your way to hit it.
Indoctrination Theory suggests that you can do everything flawlessly in ME3, but you still have a 2/3 chance to fail utterly at the end. There's only one right answer, the theory claims. Other choices are not simply unfavorable, they are flat-out wrong. Nothing else in the franchise has been that stark.
2. If Indoctrination was intended, the writers would have resolved it in-game.
Let's assume for the moment that Bioware has it all planned. Indoctrination Theory is 100% correct and all the clues were planted by Bioware deliberately. Why would they obfuscate this twist in the finished product? Take a look at what's going on right now. A significant number of players are dissatisfied. Some have sworn off Bioware products entirely. If Shepard's indoctrination played out in the game, then the story continued with Shepard getting up, seeing it through, and the races of the galaxy achieving victory, all of that would have been avoided. The writers would look clever and the players would be happy.
The Indoctrination Theory, as presented, would be terrible storytelling. It would be like Frodo almost dying on the way to Mount Doom, but then he wakes up, still miles away from his goal... and that's the end. No resolution. No ending. Only "Boy, that was a close call. But our hero is okay!" Shepard's mental state has nothing whatsoever to do with how the battle is going, and if the colorful explosions were all in Shepard's head, then the Reapers have not been stopped at all.
The in-game ending, if you take it at face value, is more of an ending than Indoctrination Theory. All Indoctrination Theory does is leave a door open that was closed so painfully by the endings as presented.
What's more likely? Given that all we have on either side are interpretations and guesses, what's the simpler solution? That Bioware didn't actually resolve the conflict, but only seeded clues, hidden for only a few players to find, about how the story would continue—clues that, once brought to light, would actually invalidate the choices of any player who chose Control or Synthesis and would also prove that their "ending" wasn't an end at all, going against all their claims? Or that, through short-sightedness, haste, or misjudgment, they simply wrote a sloppy and unsatisfying ending?