I had an interesting idea for a Star Trek show, but it was before I had ever seen the show "Firefly", and I was actually creeped out by how similar my ideas were to Joss Whedon's, despite me having absolutely NO knowledge of Firefly when I came up with them (who knows, maybe that means I've got a similar level of creativity LOL).
Anyway, my idea was a show called "Star Trek: Mercenaries". It would take us to the seedier underbelly of the Star Trek universe, where the outcasts of the federation live. I was surprised because the way I intended to portray the federation in the eyes of our protagonists was actually similar to the way the Alliance was in Firefly, only to a much lesser degree (I didn't depict them as being evil, but I did show that they had flaws and were somewhat oppresive to the outcasts).
Basically, the show would have been following the crew of the freelance starship "Orphan". The main character would be the first mate, who is a hot-shot pilot / gunslinger, who was kicked out of the Federation Academy, possibly because of his short temper, but some suspect it was his attitude about federation politics. He's somewhat scrappy, and it's not uncommon to find him in a bar fight. I noticed similarities to Captain Reynolds in FF, only my guy was younger and not a leader.
The "captain" of the ship (if you could call him that) was a klingon with a robotic arm and dreadlocks, and while he is technically the captain, he sees himself as more of a "father figure", with the crew being his family. He always makes descisions as a group with the crew, because he sees the ship as being just as much theirs as his own. He bears a few similarities to Shepard from FF.
There was also a female mechanic that I never got a chance to flesh out, but I can tell right off the bat that she would have probably been a deadringer for Kaylee. She would also have served as the ship's medic.
There were two other pilots on the ship, but I never got a chance to figure them out much, only that one was male and the other was female.
Two pivital characters in the series would have been a pair of Vulcan fraternal twins (one male, the other female). The crew finds them in suspended animation on a daralect spacecraft in the first episode, and later they discover that they are actually part of an ancient Vulcan prophecy; they are the key to defeating the Borg! In addition to being expertly trained in the ancient Vulcan fighting styles (including the use of "vi-blades", swords that vibrate at a high frequency), when the two are together they possess amazing levels of phycic power. Over the course of the show they must adapt not only to living with the emotions of the crew, but also the fact that they are in a completely foreign time period (is it possible for a Vulcan to have angst issues? Who knows). As you can probably tell, they bear a LOT of similarity to River and Simon from FF, except that they are both "special" instead of just the sister.
So basically, the show would have been about the crew of the Orphan going around looking for work (like in FF), accepting supplies and goods as payment since money is rare and not very useful (which the Federation is obviousely to blame for, in the crew's minds at least). All the while they are trying to avoid entanglements with the Federation and encounters the Borg (Alliance and Reavers, anyone?), and digging into the secrets behind the prophecy of the twins.
Really, the only big difference between STM and FF aside from STM being in the Trek-verse would have been that STM was more about dog fights, since the crew of the Orphan had specialized "combat shuttles" that were more or less peppy one-seater star fighters rigged out with lots of cool weapons and gear (giving them an advantage over the larger, slower ships that most factions, including the federation use). I was totally freaked out by how similar Firefly was to my show idea, but at the same time I was also very pleased with it. I've since become a browncoat and I love the show to death.