Well, I wonder about doing the opposite; porting characters from anotehr franchise into Star trek. A Star Trek AU.
The one we were able to mostly work out? The Mass Effect Trilogy.
Here's what we came up with (agreeing part way through to stick with species that'd been on the show, so no Hermats or Brikar);
Setting: Post-DS9.
- Shepard, Vega, Ashley, Jacob, Kasumi, Zaeed, and Miranda would be all kept human. Shep would be captain of course. Miranda would be ex-Section 31 who brought an experimental AI named EDI with her. Zaeed would be ex-Maquis, and Kasumi would still be a thief, but one who had worked for the Orion Syndicate.
Garrus would be Andorian, Liara a Betazed, Wrex an addiction free Jem'Hadar (borrowing an idea from the DS9 Season 8 novels; similarly Jack would be a Vorta who had the telekinetic abilities we only ever saw once on the show), and Tali would be a Romulan. Specifically, the granddaughter of a Romulan ex-pat who lived in a colony of Romulan ex-pats that isn't A canon, but was mentioned in the New Frontier novels. Joker would be Elaysian (http://memory-alpha.wikia.com/wiki/Elaysian).
Grunt would be a young, brash Klingon, Legion would be a robot of some kind (we had trouble with him more than pretty much anyone), Mordin an atypical Ferengi, more interested in science than profit, and Samara a Trill.
And finally, Javik would be an Iconian. Okay, they were only MENTIONED on the show, but screw it, I'm counting it anyway.
Feel free to share any ideas of your own; your own ME idea, Babylon 5, Dragon Age, BSG, Escaflowne, whatever.
The important thing here is to have fun with it, and don't be a dick to anyone over their ideas.