Oh, I don't know Ghosty...
Seems to me you over-simplified.
How about some of these:
An Intelligence campaign: You don't have to train to be an agent, or become a part of SFI to be an agent. Look at Bashir; he’s a doctor, who came within an eyelash of being recruited by Div. 31. How about L. Y.’s players?
Could: a doctor, an engineer, a command staffer, etc. be able to keep their heads, their observational ability, and other qualities while facing: political upheaval? A ruthless criminal element? And, topping these: no back-up/safety-net and no ‘massive’ resources (no true starships, best they get is a specially equipped Runabout).
Hostile Frontier/Border Patrol: Pick an opposition (the Feds got more than it share), place the PCs in ship on that species borders. Skirmishes, re-supplying colonies, escorting ‘their’ dignitaries/prisoners to/from the sector…possibilities run rampant.
SF R&D PTT: Congrads; you just became part of a proto-test team (a PTT), your job: test the latest and greatest equipment from SF R&D, ranging from star-drives to medical apparatus. And when things go incredibly right or horribly wrong (and they will :D), the players will be at the front line to see it (but good or bad)(“What do you mean ‘we’ve traveled 18 days max warp, in 2 minutes?’”)
These are just a few ‘specific’ campaign ideas, more generally:
Mix-n’-Match: These are what usually happened on TNG and DS9: the general idea was Exploration (TNG) or Space Station (DS9)…but wasn’t always the case. Murder Mysteries, Diplomacies, and other ‘distractions’ kept both crew on their toes. And how many times have we seen ‘the swerve’; where we start with one story, and end with another. The best things about these kinds of campaigns are: Variety, and each time out different players should/will get the chance to shine.
Guess what I’m saying (though cliché) is, “it’s not the destination, it’s the journey”