A very good point. Or rather, a few excellent points.
Reader interest. Every story, long or short, has its own particular target group of readers. An author may not realize it, but most of these groups are relatively small, and so the feedback and quota of readers may not be as numerous as we all like to hope they might be. This is especially true in fanfiction with unusual pairings, for example.
Flow is a big deal, I agree. It can also be hard to pin down in a way that benefits the story, and I think that most authors will readily admit that stories--especially those which consume the author's mind with plot and scenes!--are quite capable of and often trend towards overdoing things. How often do we write something that grabs us by the throat and demands to have its own way? There are ways to deal with such stories and muses, of course: a good beta is a blessing, particularly with unruly stories. And stubbornness can go a long way, too. However, for me, I find that distraction is the best tactic.
Here, I can't give you that. What do you think about this, instead? Or, Ooh, look at that! What a neat idea! Why don't you steal it away before these other muses get close? I'll let you pounce on So-and-So later as a reward.
Yes, I occasionally have to bribe my muses. Surely I am not the only one?