Well, Mr. J, since you've made yourself known, I'd like to pimp a few ideas based on my long experience GMing various incarnations of Trek :\ . Please forgive the slight (or not-so-slight) impudence

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Classes: I'd suggest making (insert government name here) Fleet-Based characters quite broad, representing professions that are similar. Have a Operations Class (for Helmsman, Navigator, Comm. Officer, ect.), Science Class (Science Off., Medical Off., Engineering Off., ect.) and Security Class (Security Off., Intelligence Off., Military Off., ect.) makes sense; names used here to signify concept. In order to have a given occupation (like Helmsman, Navigator, Science Officer, ect.) you would have to meet a prerequisite not linked to class; this is how to explain were you get officers that can handle several different jobs as we've seen on ALL Trek shows. A Commanding Class for Ship Captains and F.O.s and Military Leaders as a Prestige Class. I know that the SFB Universe has a different approch to Trek than the usual Paramount way, but this is the general idea. I'd also be sure to include civilian classes; one of many things Decipher got right that other Trek incarnations were weak on.
New Skill: In order to capture that Trek flavor of different occupations having a unique skill, I'd suggest a new one: System Operations. S.O. (which should Int-based) would have sub-categories that must be chosen when the skill is purchased and can be purchase multiple times selecting a new one each time. Sub-Cats. would be like Sensors, Deflector Shields, Communications, Transporters, ect. Don't know if D20 Modern or Future have anything like this, if not I'd suggest using it to capture the feel that a Helmsmen is different than a Navigator or Comm. Off.
Thats about it. Can't wait to see what you come up with!