I think that the standard turn-based mechanics of RPGs are a notable barrier.
I can think of two ways to get around that, without eliminating the turn-based aspect. One, however, is a far bigger design challenge, and is notably disjointed from the usual RPG paradigms - it might make a good game on its own, but may be unsuitable for integration to an RPG.
The other, however, is at least conceptually easily available. Combat roles, 4e-style. Possibly including something like the AEDU structure (if you have a skill-based system, instead of level-based, your powers or feats come from having some amount of a skill, and as you increase in skill, you get more and newer abilities.)
The analogy seems pretty natural. While, for many, the Striker, Defender, Leader, Controller structure seemed rather artificial for a fantasy character, the "tactical battle station" is an explicitly stated, and generally accepted role in spaceship combat. You might even do a fairly explicit mapping - Weapons are Striker, Shields are Defender, Sensors are Controller (consider casting false sensor images for control, f'rex) and the captain is the leader. Engineering and Sciences may be "jack of all trades" or other special maneuvers that don't otherwise fit - more like a bard than anything else. You need to squeeze in the Navigator/Pilot, but you get the idea...
If you step away from "roll a die for a skill check for a small effect or piece of information" and move more towards "I have powers that effect the ship and the battlefield" you may be able to evoke the tactical fun many folks did have with 4e. Now, the sensor guy doesn't just roll a die and scan, and the GM gives him an answer. He uses a power, that puts something like a Mark on a target, and so on.