One thing I brought up the other day was about how I felt about Tenpenny Tower being morally grey. I think why I feel that way is because of two factors: Bessie & Herbert and looking past the karmic reward.
Like I said before, Bessie and Herbert are rather nice, sympathetic characters, yet one of them absolutely has to die. By themselves this would be a rather polarizing choice, do you kill the young girl who just wants to be loved and enjoy the life she had when she was younger or do you kill the adventurer who has been to many places and learned to enjoy the company of a person who many others angrily dismiss? The problem arises from the fact they're both part of unsympathetic groups which drowns the impact of the two characters. It becomes easy to forget or dismiss a friendly character if they're part of a group made of assholes.
As for the karmic reward, I just kinda dismiss it since in an RPG you shouldn't be always dictated what's right and wrong. Key words being "not always" since it's mostly how the writer designs the quest. That's where the interest comes in, not the karmic payout it gives. I admit this is technically cheating since you'd need to ignore a game mechanic to get any satisfaction out but I'd be willing to say we all ignore portions of the game, mechanical or otherwise.
But nonetheless, dictating how "good" or "bad" your karma isn't something I care much for in side quests like TT since it can interfere with how you designed you're character. New Vegas also lightly (very lightly though) dolloped into this, with Centurions giving you good karma for killing them, yet a Legion-aligned Courier would most likely not think of them as evil.