Two areas I'm having trouble with in my skill definitions for GURPS Trek are the penalties associated with unfamiliar vessel/ craft piloting.
Starfleet uses virtually identical fully configurable interfaces for almost every aspect of vessel operation. Different work stations overlap in function and routinely back each other up during critical operations. Given a high enough security acess a crewmember could likely pilot a ship from the nearest replicator panel... certainly a senior officer could access helm control from Engineering.
It would seem to me then, that penalties for being unfamiliar with different "types" of craft should be somewhat less than usual, as the character doesn't have to deal with issues of "which is the throttle, which is the weapons"... only with the performance characteristics of a particular vehicle.
Likewise, where is the line drawn between "shuttlecraft" and "starships"... when most "modern" shuttles have warp capability?
Lastly, where does true piloting skill come into play, when runabouts and other small craft (and likely starships as well)can be voice-piloted by crewmember orders to the computer with little or no skill on the part of the "pilot"?