I'm going to talk about different kinds of people who play roleplaying games in broad general strokes. These three are, necessarily, caricatures. Most people have traits of all three general types, ranging through strong or weak preferences in all areas. However, it is a suitable fiction for the purposes of this highly, uh, imprecise discussion. In descending order of how much broken rules impact them, we have...

Type A, "narrativist", is the kind of person who plays for the story. Essentially, the game is something like a movie, or a novel, just one with a bit more interactivity involved. For this kind of player, changing the rules on them if it furthers the story is fine, because they don't really care about verisimilitude or an interesting game as much as the delicious drama. Changing the rules on a Type A player has minimal effect.

Type B, "simulationist", is the kind of person who plays for the setting. Essentially, the game is a living simulation / sandbox full of interesting things which he can poke and prod and do stuff to. For this kind of player, changing the rules on them alters the expected stimulus-response reaction he expects to get from the sandbox, as the ruleset is what he uses to interact with it. Changing the rules on Type B breaks their suspension of disbelief.

Type C, "gamist", is the kind of person who plays for the game. Essentially, the game is a game. A game is a series of interesting choices, a set of problems to be solved, a scenario to be conquered, etc, etc. For this kind of player, changing the rules on them violates the point of the game. You can't play a game where the rules change arbitrarily, unless changing rules arbitrarily is the point of the game. Changing the rules on Type C invalidates the game.

Balance in all things.

I write stories, not just character bits and notes; I have written full books and many short stories; as an ST I can aid in the telling of an epic adventure with the narrativist. But I am not telling only his story, he must share the spotlight with others and go where the tale may not follow and the rules dictate.

I research the setting, I know the flows of where the original creators IMHO want the story to go and with what details they drive it; I can explore a setting with the simulationist. But there is a story to be told and rules to follow, so some parts may have to be left for another time.

I read and research the rules, even going and lurking such forums as this so to expand my understanding of them and how others understand them. I can discuss rules with the gamist But the story is not beholden to the rules and in searching out adventure there will be times when no rule applies.