I think one of the things that hampers fan films is the need for the scripts to reference canon endlessly. If you think about it, the adventures in the original 79 episodes of Star Trek rarely have any effect on other episodes. I can only think of two times off the top of my head -- "I, Mudd" referencing "Mudd's Women," and the reference to Corbomite in "The Deadly Years" that harkens back to "The Corbomite Maneuver" subtly when Sulu exchanges a glance with Chekov.
But in most of the Star Trek fan films I've seen, they're constantly referencing minute details from all Star Treks throughout the franchise, often combining elements to make the continuity to fit the canon better and making something that was always episodic television (actually five different series of episodic television -- seven if you include the movies) into something that seems like a sprawling epic that was pre-planned all along.
Now, in theory, this is pretty cool. But in reality, if an audience isn't fully versed in every episode of Trek (sometimes including every comic or novel as well), then the episode won't stand on its own. And, if the fan filmmakers go the extra mile to bring people that maybe aren't as fully versed in the canon up to date, it often makes for some rather clunky exposition.
This is something I grappled with a lot in my writing and have really tried to veer away from. If you approach a Trek fan film as a stand-alone story in the universe, I think you're a lot better off than if you try to pen an episode that combines TOS episodes, 45, 56 and 78 without contradicting anything said in TNG 35, 42, 111 while taking into consideration what was mentioned in episode 27 of DS9 and episode 12 of VOY. And don't forget explaining why the transporters in ENT are one color, but another color in your film.
I think you should just write a good story and add everything else in for seasoning.