I don't agree with some pieces of evidence presented in the Indoctrination Theory, they seem pretty far-fetched, yet I did find it somewhat compelling because I concede that 1. Shepard can't be the
only person who is unaffected by being around so much Reaper tech, even should we consider his/her "death and rebirth" as an explanation for that, 2. the star-child's presence is suspicious; first time we meet him, it's
not in Shepard's dreams and then at the very end it turns out who he is, and that tells me that the Reapers have been "reaching out" to Shepard since the beginning. Plus the laser thing, I kind of like that explanation that the laser is not just a plain old laser that should have incinerated him/her. But as I said, I still stick to the more metaphorical interpretation, it needs no further elaboration in my opinion, but I
could make an argument for the IT if I had to. Part of the beauty is, as you say, that it keeps you guessing, IT is no different in that regard.
That's the essence of classical sci-fi right there. I write, read and study it and though it's gone through a lot of changes since The Time Machine, one of sci-fi's most important roles remains to imagine that one step further - or back, as the case may be, haha. Of course, there are many more elements to it that have become integral to the genre as it responded to the needs of the time, yet all in all I think this forward-thinking attitude is something that is so fundamental that it's just not sci-fi if a piece of work was missing it. It's definitely not the spaceships and lasers that make a sci-fi story, especially ever since we've been increasingly catching up to those once-unimaginable technologies, i.e. the story's substance must contain more to be a meaningful contribution into this collective; I think ME is definitely a worthy contribution in this regard.