A bit late to the conversation, but my 2 cents.
I totally agree with the concept that the little quirks about a game are the things that stick with you over time and make a good game great. But I really don't think killing or not killing shopkeepers has anything to do with that. Is something really a quirk if it's just a feature that was included in a 20 year old game that you really like? If PoE were really going to be great and memorable, it would need have its own small eccentricities, not recycled ones from Fallout or whatever other game.
I see where you're going, but I'd like to go further. Quriks are not what make games great and memorable; they're the lovely little details you recall when remembering great and memorable games.
Most games have neat little quirks, even most irredeemably shitty ones.