I felt like I knew what I was in for when I started the series, it was never going to have a sunshine and bunnies ending and I was very pleased with the choice - after getting over the shock, drying my tears and really
seeing what was there, of course. I also didn't think much on these details like the Normandy landing on jungle planet and I think that there needn't always be a literal, scientific explanation for every little detail. I like realism, but I love art a whole lot more, because a work like this is supposed to touch you on an archetypal level that sometimes dogmatic realism just doesn't convey (this is not to be confused with blatant inaccuracies); besides, there are so many mysterious aspects of our existence, so to call that into the tale makes it sink deeper in a way that we only get tastes of up until that point, and that only depending on what kind of player we are.
Besides, traditionally science fiction is supposed to be about so much more than how accurately we can imagine some scenario in the future, and also there is an element of an almost supernatural, magical mysticism that has long been associated with the masterpieces of the genre which I think has a very important role. I would agree that in some instances "hocus pocus" solutions just kills a story, if it's not realistic enough, yet at the same time I think it a pity if a story doesn't take a leap and go to unexplored places, when the whole point of science fiction is to do just that. Not the only role, but a really fundamental one. Sure, it can be argued that ME3's ending was one of those that brushed realism and kind of missed with these scenes, but I disagree - right from the point of saying goodbye to your squadmates, everything becomes very surreal, supercharged and dramatic and I actually found the starkness of my situation to be poignant and fitting. It wasn't meant to be an easy decision.
Anyway, if we really want to argue about the realism of the ending... I'm kind of sold on the indoctrination theory. It just... fits.