[ME3] The Intentional Fallacy
Along with the discussion of the unsatisfactory finale, some theories have sprouted with the intention of providing a more complex, suggestive theme to the ending, which would bespeak of subtlety and artfulness on the part of Bioware. It is difficult to maintain such a view in the wake of subsequent events (Bioware bending to the fan's will and promising new DLC that would provide the expected closure). Had Bioware not submitted to the fans' demands, still the discussion of the indoctrination theory would have been futile.
A quick summary of the theory: Shepard would have been indoctrinated at some point of the story, usually after the Reaper beam, right at the ending, and everything that follows is either a dream or a Reaper's contrivance to force Shepard's final decision to their benefit.
I consider this theory an unrealistic expectation on the fans' part. There are some instances of ambiguity in the story that allow a symbolic interpretation, like the final scene in which Shepard is almost stripped of agency due to bloodloss and mindcontrol. This is suggestive of the unreliable narrator of which the fan theories speak, but most likely it is a mere emotional device that intends to sunder the player's image of godlike Shepard.
Some people have argued that it is clearly not Bioware's intention, although little has been said either by Bioware or by fans to explain why this theory is wrong (if you think such things can be right or wrong, which I'll argue later). To me, the theory is disproved due to a fault in consistency. The unreliable-narrator hermeneutics is not supported by the work's tone and structure. Mass Effect had until then never attempted any plot exposition that was not direct (like showing videos of the Cerberus scientists at various locations degenerating because of indoctrination, instead of silencing the facts and allow for the player to draw her conclusions based on the environment; that simply had never been done), and surely Mass Effect had not had any dream-like sequences, any instance of unreality, ambiguity. Shepard's dreams are merely dreams, by what we gather from our previous experience of the game.
Perhaps you have played Final Fantasy VIII. I didn't, I wasn't fond of JRPGs, partly because their stories seemed purposely convoluted, undecipherable; which was precisely why they were pregnant with alternative theories that tended to read into them in a symbolic way. Regarding FF8, I read a theory that posits that Squall had been dreaming half the game since his encounter with Edea, who might have killed him, instead of just hurting him (with a gigantic shard through the chest, of which he recuperates with no further mention). The theory is supported by the game's general vagueness and dream-like quality (like most FF games), which is exacerbated after this encounter. It is a very curious read which had me amazed by its allied rationalism with fantasy.
In order to ascribe to either theory (the 'official' one, which is the literal game, or the dream), you usually go through a process of authorial invocation: how was the work intended to be read? Could SquareEnix/Bioware have thought of such an interpretation, and fostered it? It would require, as I mentioned before, a high degree of subtlety, or else the edifice of dream/indoctrination would be too evident and its impact diminished by its bluntness; no longer a symbol, if exposed. Not only you might invoke the author in this question, but you will also consider whether she would be capable of such finesse. You don't question the work, you question the author, her mastery of the craft and of the intellect. That is, unless you a) respect the author, b) respect the narrative genre (since when videogames exhibit such degrees of artfulness; in contrast, -good- literature is expected to provide complex symbology, c) the work allows for such an interpretation (the author imbues her work with a subterranean current that can be dug out. I'm placing an emphasis on the active verb here, as symbolism requires an attentive reader, 'digging out' its meaning beyond what is literal).
You may also counter this preconception. One might brandish the theory of Wimsatt and Beardsley, called 'the Intentional Fallacy': the mistaken belief that what the author intended is the 'real', 'final' meaning of the work, and that we can or should know what this is (Wimsatt and Beardsley 1995). So, it is not the responsibility of Bioware to give meaning to their work, according to such statement. I don't quite agree with it, although I admit that it has its advantages, particularly in the field of psychoanalysis, as the work of an author is also product of her unconscious, and therefore it conveys much more about her mindset and that of her generation than she thought. There are no 'wrong' interpretations: As long as you provide facts to your theory, it is valid, out of the author's reach. There have been counterarguments to Wimsatt and Beardsley's idea, but if you wish to ascribe to it and see the work of Bioware without an authoritative perspective, you might.
I won't, because I have to admit that I am prejudiced against this work and its author, and thus I cannot take it seriously when they themselves don't know how a character might look like, when they seem to have improvised the story (Crucible never even hinted until the last game, not even by the prothean beacon of ME1), when they had been very vocal about plot-twisting decisions and their consequences (and yet they revived a rachni queen in case you had killed the first one). Such game cannot have allowed the nuances of a symbolic interpretation, not even subconsciously.