User blog comment:The Milkman/Everybody Shut Up./@comment-4933332-20120423072223/@comment-4950455-20120423101105

What I'm saying is that Shepard being indoctrinated, the game can still continue with the reapers losing and in fact I do believe the game probably be more dramatic and entertaining with that option rather than breaking free of indoctrination and then beating the reapers.

Right - that's what you believe. For a while now, and largely unrelated to this whole ending debacle - although it's admittedly the only reason why I give any credence whatsoever to the artistic integrity argument - I have been growing very tired of people couching their personal preferences as the objectively best decision. As such, while you may personally appreciate the idea of a Shepard-is-indoctrinated route, you don't really have the right to claim that's actually what Bioware should have done, which is the vibe I'm getting.

Furthermore, I'm not sure I agree with your claims about "bad" choices. The decision to spare the "fake" rachni queen is the only case where I can think of the game presenting a choice as absolutely a mistake, and the situation there is very different - you are given actual reason to suspect that trusting the queen would be a mistake. It's not a "choice" so much as a test of the player's intelligence. That doesn't really crop up with what's presented in the game as far as the indoctrination theory goes. There would need to be more clues besides petty nitpicks like "magically appearing trees" and details buried in the Codex (that aren't even in the ME3 version, IIRC) for it to really be fair. To quote the OP again:

''My retort then, is did you think of that then? Did you immediately come to the realisation when you made that choice? The choice for which you have no understanding? Did you stop and think it was all a dream? No, you probably didn't.''

Frankly, I think he's being far too generous by saying "probably". Yes, the player should have a chance to be fooled; no, that chance should not be a guarantee. I doubt anyone would have even considered the indoctrination theory - even with the same "evidence" in the game - if that final so-called choice hadn't been such a mess that some other explanation was desperately sought for it.

We're then left with two ways of seeing the theory. If it's taken solely on what's in the game, then it would have been a writing failure nearly as bad as the current endings. There was no real way for the player to realize that Shepard was being indoctrinated; no evidence or foreshadowing besides the most obscure sort. Even if we assume in this hypothesis that the other problems with the theory - the fact that you can be forced into Destroy with too low EMS, the lack of any follow-up - didn't actually exist, this still would be manipulative and unfair to the player, disregard the series' themes of choice, and probably draw a significant backlash in its own right, though admittedly not as much as the current ending.

The other option is to venture even further into the realm of the hypothetical and assume that there had actually been genuine hints and foreshadowing - not just scraps grasped at by people desperately looking for answers - that Shepard was being indoctrinated, enough so that it would be realistically possible for players to guess it in advance. This could indeed make for a very nice twist ending (though I think my issues about choice still stand), but it's not what we got. As such, I have a hard time seeing the appeal. I'm happy if the idea you imagine of a Shepard-is-indoctrinated ending appeals to you, but it's essentially personal fanfiction rather than anything supported by the game.

tl;dr: Don't confuse an idea you find personally appealing with what would be best for everyone, particularly in a game that's about choice. As things stand, the evidence for the indoctrination theory is obscure enough that, were it true, it would be pretty bad writing on its own.