See this is something I've been trying to figure out for a long time and recently I think I've picked out why I think the moral choice thing has never been bad. I Know the character before I start. With every play through I don't just good/bad/neutral, I think of the character themself in context. (This is more for anyone who cares skip to the asterisks if you don't.)
Using ME and ME 2 as my example. I had four save games coming into ME 2.
Shep 1: Sole Survivor and Colonist; I played paragon because I believed this was the kind of character that had seen bad and would never settle for anything less than saving everyone they could, sparing anyone who asked for mercy and giving people a second chance. Always willing to talk if people they were.
Shep 2: Spacer and Ruthless; This Shepherd was Renegade. Always meeting force head on, no one getting the chance to surrender, everyone was a potential threat and treated like that. No authority would stop him, you either helped you stayed out of the way. He was worth fearing because he followed a straight line to his his objective and if you were in the way he didn't give you the option to move.
Shep 3: Earthborn and War Hero; This one was neutral-ish trending to good in good/bad choices. He'd grown up in slums, run with a gang, commited crimes but only because that was the only open option until he could join up and cast off that life. He knew about the grey of life in places that weren't perfect like the Presidium, he knew everyone was a little dirty because that was the only way to live in that kind of place.
*****My basic point is other people don't seem to really put anything of themself into their Avatar. If you put yourself into the character and make an honest choice from the way you look at them the choices aren't hollow. That being said there are choices that I can never find justification for like the Samara Mission in ME2. I can't build a logical reason for Shepherd to make the Other choice.
