I'd like to start out by saying that Fallout 3 is an amazing game with good replayability. I've (sadly) logged on many hours in that game.
And though Fallout 3 is an amazing game, there is some stuff that just bothers me to no end.
First and foremost, the way the Lone Wanderer dismisses Fawkes.
"You're fired Fawkes, stop following me around."
??? Isn't my character supposed to be amazingly nice? It just sorta leaves a bad taste in my mouth.
Secondly. The endgame when it says stuff about your character not being a true hero if you send Fawkes, who's immune to radiation in. (or Charon I guess. I keep forgetting about him) I guess it's just a reason before honor thing for me.