Maybe that's not the best example anyway. A director should be able to do something about the "Row, row, row your boat," crap. You wouldn't defend that, would you? If they make changes that the producer doesn't like then there's always a chance they could be forced to re-shoot it unless the shooting schedule or money is really that tight, but it seems unlikely that they wouldn't be allowed to change that.
> Itís bad but there are worst Trek episodes or movies out there
Counting movies and TV together, I think it's in the 10 worst. Nearly every major plot point has a massive plot hole in it.
-Sybok's mind control powers make no sense, and his hostage plot makes no sense. They could have just said that he can control people's minds, but instead they said that he can cure people by healing their secret pain. Does that make sense to you? So most of the Enterprise crew, along with the ambassadors, all have pain so bad that they'll commit treason to have it removed? You'd think that for most of those people the treason would cause them more guilt/pain!
-His plan only works because The Enterprise, which is on Earth, is the closest Federation, Klingon, or Romulan ship to the Romulan Neutral Zone, which is ridiculous. And it also wouldn't have worked if they didn't have only a skeleton crew on board, and if their transporters hadn't been broken.
-And the who plan is unnecessary anyway. Why can't he just heal some ship captains inner pain and get him to fly him to the great barrier? Why does he need to take hostages?
It has other problems too, I'll let Roger Ebert handle the next one:
Another irritation is the way in which we meet apparently major characters, including those played by David Warner, Laurence Luckinbill and Cynthia Gouw, who are introduced with fanfares of dialogue and then never developed or given anything to do. The entire movie seems crowded with loose ends, overlooked developments and forgotten characters, and there are little snatches of dialogue where some of these minor characters seem to be soldiering on in their original subplots as if unaware that they've been cut from the movie.
And to your earlier point, the fact that Shatner cared more about showing Dante's Inferno than to fix basic problems like the one in Ebert's quote really speaks to his incompetence.
Also, there are other bad episodes that I doubt we'd see mentioned again, they're just not made a big a deal of. For example, in Turnabout Intruder they say that women can't be captains in the TOS era (even though Pike had one as first officer). Don't you think that had been retconned out by TNG? Of course they retcon details all the time, but you need that detail to make sense of the plot of the entire episode.