You mean the reasons aren’t obvious?
About as obvious as a sledgehammer to the groin, dramatically speaking.
Oh, I thought you were disappointed by the lack of justification.
That's my point. Discovering a moral lesson and having a moral lesson preached to you in episode format are two VERY different things. I've come to find that kind of irritating in my latter years... patronizing, even.
I think it's a little like the changing use of technobabble in later seasons of TNG and Voyager. TOS was very tech heavy as well, but the technology was always in the background, supporting the characters in their struggle for success. By the time we get to Voyager we're bouncing phased polaric tachyon pulses off the starboard impulse manifold in order to produce a resonance attenuation of the space time continuum. Yes, Rick, I know you think I'm a retard, but I DO notice when you're just making shit up, and I DO notice when you're trying to preach a morality tale. The story has a lesson, I get it; just focus on telling the fucking story and let the lesson take care of itself.
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I wouldn’t rule out positive reinforcement though.
Neither would I. Except in the context of a TV show, where "positive reinforcement" is identical to "rehash." That's kind of what I mean by preachiness: the lesson of "Let that be your last battlefield" doesn't become a whole lot more poignant if you change the black/white guys to some religious fanatic suicide bombers.
In the end, you can draw any moral lesson you want from any episode of Star Trek, but if the characterizations and interactions are weak, it's just a bad episode. I would
invariably prefer a good episode with a shallow message to a bad episode with a good message. To quote another of my favorite shows "We go to church to learn all that stuff, we go to movies to be entertained."
But I am not suggesting ST should go out of its way to contain moral lessons at all.
You're not? Because that's what would be required for Kirk to show mercy to Nero against his own explicit maniacal hatred. The simple fact is that at this point in the movie there simply isn't enough screen time left to deal with that kind of outcome in a halfway reasonable way; if Kirk rescues Nero, you now have to take the audience through some kind of resolution involving what is to be done with Nero and his crew, what happens to the ship, how will Nero answer for his crimes, how does Spock feel about having to rescue the man who murdered his mother, etc etc.
It's simply easier from a dramatic standpoint to avoid all that red tape and just
kill him. Morally, it's not something the average person would question considering the kind of Mayhem Nero's been perpetrating on the universe since the moment he entered it. In short,
capturing Nero means you still have to deal with him by the end of the movie (or in the next one, which would suck). Killing him gets him out of the picture, and we can all move on.
I don’t agree with that. Moral issues seemed to keep cropping up in TOS. It kind of went with the territory.
Of course it did; reality is that way too, you may have noticed. But TOS was fundamentally about a ship named Enterprise and three officers named Kirk Spock and McCoy; now matter how absurd those episodes became (seriously, TOS had some pretty cheesy premises even for the 1960s) it was always entertaining to watch to the solutions generated by Kirk, Spock and McCoy on their ship named Enterprise. The moment the story stops being about characters and starts being about situations, you run into trouble; the characters become interchangeable, and you stop caring about them.
Take "Mudd's Women" for an example. The moral lesson is so simplistic that Jim Kirk states it openly: "There's only one kind of woman. You either believe in yourself or you don't." The entire episode leading up to that moment is full of character moments, jokes, glances, seduction, arguments, passion, theatrics, villainy and wit, but in the end it's only Captain Kirk's unadulterated sneakiness that brings about that moral lesson.
As you say neither they or their solutions have to be explicit or rammed down our throats but that doesn’t lessen the potential drama.
True, but a writer is, at the end of the day, a storyteller, not a preacher. His job is to tell a good story, not to moralize his audience. So in Mudd's women we don't get an extra sermon about the evils of drug abuse or about how wrong it is for Harry Mudd to be trafficking women to alien worlds, or his extortion of the Enterprise to cover his own ends, or about how wrong it is to violate space traffic laws and put other people at risk. It's alot more efficient to simply throw Mudd in jail and be done with him. Same again for the salt vampire: if we had another two hours to kill we might enjoy a very entertaining debate about whether the creature was really malevolent or just hungry, whether it should be destroyed or punished or returned to its planet or whatever. But we don't
have two hours, so set your phaser on kill and let's end this thing.
Accepted. But I’m suggesting it actually undermined Starfleets moral underpinnings and presented doing so as perfectly OK on more than one occasion (four at least).
I don't know that Starfleet has that much patience with genocidal maniacs. They were perfectly willing to eradicate the Borg, for example.
Yes, I saw that coming!

I guess I should have added "if it seriously compromises the brand."
"The brand" is an entertainment product, my friend. It doesn't "compromise" anything at all unless it flops at the box office. So Star Trek Insurrection may have be morally pleasing on a number of levels, but it doesn't help the brand much if the numbers flop.
Besides being an all around crappy movie.
Although I was seriously put off by the issue I mentioned I don't deny STXI has a lot of potential and although there are quite a few things that could be improved, none of the others are really deal breakers for me.
Has that not been the case for every Star Trek movie you have ever enjoyed? Even in TOS there were plenty of things they could have done better; that's precisely why we have TOS-R, and is also the reason why so many TOS episodes were later recycled in TNG episodes and/or movies (TMP is pretty much the cinematic version of "The Changeling.")