On the corrections on my take on things: I was just watching my wife play, and certainly missed some things. I appreciate the attempt to make sense of it, but it's still not much better a plot... like you said, it's pretty unclear.
On the "hit-or-miss" glitches: like I said, my wife had maybe 10% of the ones I did, and really enjoyed the game. I just found that every time I tried to put any time into it, something would go wrong, and it had failed to grab me in the slightest by the time I was through with the hallucination missions. I'm not sure it would have gotten any better, but if I had a glitch in nearly every mission up to that point, you have to see where I'd be like "y'know what? I got other stuff to play..."
What was wrong with your Mass Effect? I had some weird texture issues my second playthrough...