With Butch and the radroaches, remember that your life is already in peril and you need to escape the vault. Trying to save Butch's mom is clearly a good-guy thing to do. I am pretty sure that we can turn Butch down without being mean about it, so that not trying to save his mom is not clearly being a bad guy.
Harold is unhappy with what life has brought him, and he is pessimistic about his life to come. Harold is no longer fully human, but he persists in seeing things from a human's standpoint. He has the capacity to enjoy a happy life despite being rooted in one place. We are given an opportunity to help him achieve an optimistic outlook.
You assume that Dr. Lesko's work is useless, so you bias yourself against it. Assuming that his goal is feasible, should his experimentation be permitted to continue? Has he finally managed to put ample safeguards in place? Is the potential of reversing dangerous mutations worth some risk? If so, how much risk is too much? Is Dr. Lesko on to something, or is he only wacko?
Even when he isn't pulling the trigger himself, the Overseer is ordering others to pull the trigger. This man ordered the death of one of your good friends, and he is determined to have you killed just for being your father's child. We can find evidence that the Overseer is seriously contemplating having Beatrice put down for being senile. We can also find evidence that at least some of what the bullying Tunnels Snakes do is done on his bidding. The man appears dangerously unstable, so the vault might be safer without him.
You expect me to enumerate every single gray choice in the game while you need only enumerate a handful of black-and-white ones? That ain't fair.