I think that's a false dichotomy. The limitations of a setting can be important to a story -- for instance, if a character is too far away for help to arrive in time. Naturally you want the audience to pay more attention to the immediate emotion of a story, but the storytellers should keep the realities of the setting in mind when plotting the story.
I guess I'm saying that if some distance or timeframe somehow ruins an episode, perhaps because the writer wasn't fully aware of Trek space travel capabilities, I can forgive it.... maybe.
Having an established maximum speed and the time it takes to travel certain distances makes sense but it can also be limiting. Perhaps those limitations and cabapilities of space travel should almost be taken episode by episode.
If something in a previous episode contradicts the next one, that's not fun but should one ignore it if the episode is great?
Speeds and distances shouldn't be too precise, too much details can hurt storytelling but having somekind of established guideline makes sense.
Even if I don't make much sense with this post.... =)
I guess Star Wars might be a good example where ships can travel massive distances in no time. Star Trek is better with that.