Arc.Smiloid,
Both of the models you mention have things going for them.
A. is like Starfleet Command (a great, real-time adaptation of Star Fleet Battles, IMHO) which provides for a seamless and thus more-"realistic" simulation of starship combat. Assuming that players can set the speed as low as desired (as in SFC), this won't result in lack of time making for rushed/poor decisions (a leading reason why RTS games can be disliked by turn-based players, I believe).
B. is the Combat Mission model (I keep finding myself relating this game to SE4, though I don't plan it
). CM provides a really fascinating mix of your "omniscient" orders given at the start of each minute-long turn as they're interpreted by your troops (a tactical AI that can partially or totally take over depending on how the turn plays out) during the turn.
As big a supporter as I used to be of total player control in a turn-based environment (and still am, compared to the frenzied click-fest that substitutes for "strategy" in most RT'S' games), I must say that SFC and CM have changed my view, and I now enjoy the non-turn-based structure they offer, in addition to turn-based games.
Well, that's a bit off the subject: the "I move then fire; you fire then move" tradeoff of the non-simultaneous/non-impulse movement system in SE4 that can result in the combat problems mentioned. AFAIK, the turn-based game that best corrected this was Star Fleet Battles. By breaking movement down into a per-hex/impulse basis and allowing fire at that level, it prevented the sort of excesses present in SE4 (and Starfire before it, along with every other tactical all-move-then-fire or fire-then-all-move or fire-at-will-during-movement system) without going real-time. Something like opportunity fire would do this too, but wouldn't be as thorough a solution as impulse movement. However, it might be a worthwhile trade-off since today's players don't really expect to need the patience that impulse movement requires (myself included, though I was happy with impulse movement 18 years ago).
Just my two centi-credits...