I think the best way to learn about the theory of scriptwriting is to just dive in and read some books.
A while back I read three in a row, and they were really helpful to me. I'm not saying that I'm now an awesome writer, but I think I have a deeper understanding of how to go about it where before I was running on mostly intuition and my half-forgotten memories of film-school.
The three books I read, and fully recommend are:
Essentials of Screenwriting by Richard Walter
Save the Cat by Blake Snyder
Story by Robert McKee
There has been a lot of talk about structure here, and to me, it's character
that is more important than structure. You must present characters that the audience will care about and identify with. If you can't do that, it's game over. I think the STORY book by McKee covers character the best, as it ventures a lot into psychological components. I don't want to quote these books endlessly, even though I have dog-eared them. You really should read them.
I think a lot of the fan productions got started for reasons that are totally different from a budding screenwriter or producer. They were started more of the natural extension of cosplaying at conventions. They were not done because the people involved had a compelling story they wanted to tell. It was about role-playing and paying respect to Trek, and I think that is creatively limited.
If you have a good story to tell, what setting you place it in is meaningless. If you watch some of the TOS episodes, the premise of Trek is pushed and pulled in the most unusual directions. By the time we got to the TNG-era shows I think the leeway collapsed down to a very narrow trench, and it helped kill the franchise.
I know some will disagree but to me what constitutes a good story more than anything else isn't blazing action, it's characters that I care about who are put in tough situations and who do the right thing
Here is how this has often played out in Trek...
Think about City on the Edge of Forever. Kirk is asked to choose between himself (true love) and the greater good of the fate of the timeline. He has to make a tragic sacrifice. That is thematically the same as Spock sacrificing himself to save the ship in Wrath of Khan. And then Kirk and company repay Spock by sacrificing the Enterprise itself (and at the time, they thought their careers) to save him. Or what about Decker sacrificing himself to merge with V'Ger? What about when Elizabeth Dehner (played by Sally Kellerman) is convinced by Kirk to turn back to the good side and attack Gary Mitchell? (That scene of redemption is not that different from Vader zapping the Emperor in Return of the Jedi)
So to me, it's not structure that matters most, it's characters, the dilemmas they get thrown into, and the choices they're forced to make that define them.
Even Galaxy Quest had good character motivation. It wasn't just a cheap excuse to sling jokes at Trek. The moral of Galaxy Quest was that anybody can be a hero if they just believe they can do it. The aliens believed that the cast of Galaxy Quest were heroes, and the situation forced them into acting as if they were heroes until they discovered they could "fake it 'til they make it". It's actually a very uplifting story despite the jokes about Sigourney Weaver's push-up bra. The frame around it, even whether it's a comedy or a straight drama, rated G, PG, or R, is not as important as the power of the underlying message.
What middyseafort was saying about Everything's a Remix is also true. Every sort of traditional Trek tale has already been told. You have to tell it a different way or somehow bend the rules. I did not like how JJ Abrams did this in the 2009 film, but I understand the motivation to try.
Just as Khan mashed up Horatio Hornblower and TMP mashed up 2001, I decided to mash-up Revenge of the Nerds and Fast Times at Ridgemont High, among other things. Maybe I'll be the only one who likes my pickles-and-ice-cream mixture, but at least I'm trying to do something original.
The other thing the screenplay books emphasize is that whatever you write has to come from you. If you try to run away from yourself, it will come across as false. Imitation is false because it's not of yourself. A remix can
be of yourself because it's the way
you piece the collage together that makes it greater than the sum of its parts. I have gotten a lot of criticism, some of it constructive, and some of it not so constructive, about what I'm doing, and yet I've reached this point where I feel that my approach is already very finely tuned to my own sensibilities, capabilities, and the bounding box of my chosen toolset.
It's true that people become too close to their own work and so they worship every frame, and you can't close yourself off to criticism. But I also think you can't please all the people all of the time, and Trek fans can be merciless.
If I feel I make something where I can sit back and watch the final cut and really root for the protagonist and hiss at the antagonists, then I've succeeded. I need that long build up and then the fist-pumping moment where the character, who has his or her back up against the wall, can either do what's expedient, or do what's right, and they do the right thing.
I think that's why of all the fan trek I've seen, I like Aurora the best, even though the pacing is slow. The technobabble in the middle of it about alternate reality was not the heart of the story. It's a story of a woman trying to move beyond a traumatic incident in her life and reconnect with her family. When people really get engaged with a story, it's at this innermost level, and the rest of it becomes almost inconsequential.
Maybe that's not how every successful story has to be, but that's the sort of story I like watching and the ones I want to tell.