Easily the best subplot in the game. I'd have better theories if I read the novels.
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Definitely. Side note: did you notice how it said choose your mass effect history and then just asked what Shepard's gender was? Did I miss something in the story or was that pointless? Or maybe there will be something in future DLC? As far as I could tell they never refer to Shepard's gender they just refer to him/her as Shepard in [spoiler]the unlocked memories about the Reapers[/spoiler].
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I think Liara refers to the gender in one of her logs.
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That seems like a tiny insignificant thing to have you choose at the beginning. Unless like I said there'll be more in some DLC.