Every TOS movie has given us a Big Idea or Big Lesson in its storytelling.
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What is the Big Idea or Big Lesson in STXI?
I don't know, what do you think the overly-obvious, obnoxious hit-you-over-the-head-with-the-meaning-of-the-film-because-the-writers-are-no-damn-good-at-subtext "message" of the film was? Because I surely would like to see more hackneyed allegories and obnoxious morals of the story to get in the way of actual storytelling.
Why shouldn't a story be about ideas? If it's just about beating bad guys, that's certainly not unique to ST and not very interesting as it's obvious that the good guys will win.
I've got no problem with a story being about ideas. I have a problem with a story being about Big Lessons. This is Star Trek, not Aesop's Fables.
Most of the time, when Trek tries to do Big Lessons, it just gets in the way of storytelling. It comes across as being more akin to a political tract or thesis than it does an actual, relevant story.
The best way I can think to describe it is the difference between Star Trek V: The Final Frontier and Star Trek VI: The Undiscovered Country. TUC is about ideas -- it's about the end of an era of history, and how it affects people who have always lived under certain political realities suddenly having to adjust to living in a world that's nothing like what they grew up in. TFF, on the other hand, is about a Big Lesson, and it beats us over the head with it -- Kirk is thinking about death and there's this crazy guy looking for God and then they find God but God is not God because God is in our hearts.... It's an absolute mess.
With the TUC, the deeper meaning of the film is seamlessly integrated with the character and plot arcs; it's just what the film is about. With TFF, the plot and character arcs are built, artificially, around the Big Lesson, and it doesn't flow organically from the plot and character arcs. In TUC, even when it's being really obvious in its politics ("Colonel West," "Only Nixon could go to China"), it just works as the political reality of the characters' lives. In TFF, it just feels like Shatner is taking a baseball bat to your head saying, "THIS! IS! DEEP! STUFF!"
As for ST09...
It has a deeper meaning. It's about how we react to tragedy and pain, about what kinds of people we choose to be in the face of horror. And it's about learning to get past conflict and dislike to form a real and lasting friendship. And, most of all, it's about the idea that there's a better future ahead of us. And it manages to be about all these things without letting them get in the way of the story.