Okay, look, when an author makes a total mess of a plot, after a certain point the only way to fix things is to just say "it was all a dream" and pretend that a bunch of stuff never happened. The ending is a mess in terms of plot holes, and I agree that "it was all a dream" is about the only way to make the endings "make sense" given what we know about the universe.
But.
If the indoctrination theory is true, then Sheppard never made it to the citadel, and never activated the catalyst. This means that, based on the game I bought (and not some hypothetical continuation), the reapers win, everyone dies, and the *entire trilogy* was one giant "
shoot the shaggy dog" story. That would be about the worst thing an author could do to an audience. At least if the endings are taken at face value the Cycle is halted, and *some* life has a chance to go on *somewhere,* so Sheppard's sacrifice isn't in vain. Heck, even some (all?) of our squad lives on (though it's not clear how long they would last on that planet).
The alternative is that the game isn't actually over, which would mean that the game was actually ended with *absolutely everything* unresolved, and an "ending" scene which was intentionally confusing, ambiguous, and distressing. There is no *conclusive* evidence for the indoctrination theory; all the evidence is circumstantial. So we would have to believe that Bioware intentionally released a game which
had no ending, and offered the player no clear evidence that an ending was forthcoming. This would be an absolutely cruel way to treat the fans of the series, and would show tremendous disrespect for us.
There are three possible ways this ending was "intended." One, it was meant to be taken at face value. Two, we were meant to understand that Sheppard fails and the Reapers win. Three, it was never intended to be an ending, and the actual game terminates before any actual ending or resolution has been reached.
All three of those things are bad. I don't want to argue over which would be more offensive or cruel, but none of them is an acceptable way to treat paying customers, particularly given that this is the final game in a trilogy (as opposed to a standalone game, where this sort of thing would be merely "bad" instead of "horrifying"). The third is dangerously close to outright fraud (i.e. we were sold a product and told it was complete, but it turns out it was missing parts, and the seller knew that going in and lied about it).
It almost doesn't matter which one of these interpretations is right; in every case, it's bad. Personally, I tend to give Bioware the benefit of the doubt and assume they didn't *intend* to cause 95% of their fans to feel terrible. I assume that, while they may have made a mistake, they are not cruel. This leads me to the "face value" assumption; the authors had an ending in mind which they thought would satisfy us, but failed to convey it well, and we were left with an ambiguous, plot-hole filled mess instead.
Hopefully they'll give us some free DLC that will give us a more satisfying ending. But personally, I hope the "false ending" indoctrination theory is not true. Because I really don't think I could forgive Bioware for that.