Ok, here we go.
Really, this sort of story is always going to have a lot of discussion and plenty of plot holes which could be proven and unproven, but at least we're discussing it, which is kind of fun in and of itself. Like the Terminator movies! I prefer what I consider to be a well-executed story like this than a massive bed-shitting like in Mass Effect 3.
I am sooo tired and a lot of that probably didn't make sense. I seriously just went out for lunch like an hour after waking up, went home, and played pretty much all day. I feel kind of out of it.