Meteor, black hole, and galaxy for Aubrey please!
Thank you! These are fabulous questions!
Tagging @mtreebeardiles for meteor for Aubrey (who I assume you were asking about - I'll address John A. for you on your post).
Tagging @laelior who asked for galaxy for Aubrey.
Meteor - Does your Shepard have any quirks, strange mannerisms, annoying habits, or other defining characteristics?
So, because Aubrey is the clone Shepard, because his entire existance is due to Cerberus interference and a petri dish, his entire life has been nothing but stress after stress after stress. I honestly don't understand the technicalities of the medical/scientific stuff involved in creating a clone - let alone one who is ready to go in such a short amount of time as Bioware set up. To make it easier for me, I'm basing quite a lot of my understanding off how Grunt was created and educated in his tank. Neural impants are another thing I don't have anything more than a cursory understanding of, so same thing. (fair assumption or not, that's what I'm going with because I understand Grunt's situation just a teensy bit more than I do the human clone thing)
Suffice to say, Aubrey ends up with a few mannerisms and habits, good or bad, that are unique to him, but I'm only going to give you one of them here because I'm still working on figuring out what they all are.
The major one develops specifically because of Brooks, but isn't limited to situations just with her.
When Aubrey 'wakes up' (for lack of a better term), he is overwhelmed, to put it mildly. Without Shepard's experiences or background when he wakes up, he has no coping mechanisms in place to help deal with it all. On top of that, he has Brooks manipulating him for her goals/desires from the get go. He goes along with it at first for no other reason than it seems the easiest way to buy himself time to figure out what the hell is going on.
That said, it doesn't take long to realize what she wants of him isn't something he is willing to give - but he cannot find a way out of it; not yet, anyway. So, when things get too hard, too harsh, when Brooks is on his very last nerve (it doesn't occur to him to try to deal with her himself, and even if it did, she has too many security measures in place), he takes to tapping out different rhythms with his fingers. Depending on what kind of situation it is, you may get a rhythm from a specific song whose mood fits that situation, or (unknowingly) morse code for SOS.
You'll see later in his stories that Brooks isn't the only one who triggers this kind of response; it usually is an indication that Aubrey has reached his limit and if pushed beyond it, well... I'll just point out he is a biotic with very limited training.
Black hole - What is your Shepard’s greatest fear?
Hmmm... very good question. Considering the way in which the Clone comes about, I'd imagine Aubrey has quite a few of them from the moment he wakes up. That said, jumping ahead a few years (and since the stories will be about him) and based what I know about him right now, I'm going to say his greatest fear is that he will forever be mistaken for John A. and will never be allowed to move beyond that.
Galaxy - Under what circumstances do they find killing to be acceptable or unacceptable?
The way Brooks trained him, Aubrey sees his sole purpose as to kill Shepard and replace him by any means necessary.
Problem is, no one ever asked what he wanted. Had he been able to break free of her and the 'mission', Aubrey would have run - to where, he had no idea, just away - but her control over him was tight. Even after the mission fiasco, even after eventually finding out that Brooks died on that ship, he still expects her around almost every corner, just waiting to pull him back under her control. She, he'd kill in a heartbeat; no thought, no regret.
Shepard, too, would be an easy kill, at least once he finds out more about John A. himself. It's difficult for Aubrey to put into words why, but he knows enough about the man, has to deal with enough of it when he's mistaken for him, that he is aware he deserves it - and that has nothing to do with the fact that if John A. was still alive, it would end up with one of them dead anyway.
Beyond that, circumstances vary. He develops a healthy sense of self-preservation - despite the confusion he goes through at first - and will defend himself. And, while he isn't outwardly the "I must defend the defenseless", he does develop a sense of that as time goes on. (not going to give specifics as it has to do with his story) By that point, he is cabable of differentiating between acceptable and unacceptable without the chaos that is the beginning of his life influencing his decisions. (if that makes any sense whatsoever! lol)