I recall ST BotF space battles as pretty cool thou crappy graphics, but that was the sign of the times. I have some StarTrek game at home I played a bit thats less like a strategy game, more adventure, but it has good ship to ship combat. Its more or less realistic when it comes to most aspects of what sci-fi fans understand as space warfare. You got shields and boardign and tractor beams. Using all kinds of weapons and tryign to outmanuver the opponent, altough on a 2D field (Ships are fully rendered you just cant go up or down). That's a pretty cool space battle for a small scale engadgement. But if I had to control multiple ships that totally wouldnt work.
Yes I played Conquest: frointier wars, really good game IMO, but I am tad weak at micro in RTS since I've come of the advanced age (20+). It's really more for youngsters and their sharper minds. The space battles there where ok thou it's not realistic. I would think that in a realistic battle one would try to deal a spread out damage to disable as many ships as possible. In almost all RTS the idea is opposite where you want to focus on one ship at a time because the ships have the totaly bogus property of 100% functionality no matter how busted up they are. Down to 1% hps and can still fire and move at 100% the rate. Thats the big problem with amost all RTS games. It's not really strategic.
In Moo2 atleast there was loss of functionality as ship took damage. Firing your guns one by one hoping the crutial system is damaged like the targeting computer or engines and spreading the fire out made it more of a strategicly realistic game. Altough the taking of turns between players took away more realism. Still it was pretty good. Thou it wasnt the only game where the ship suffered functionality problems due to damage during battle, few other did to. Off the top of my head I can name space empires. But there you didnt have all the components of ship to ship combat, the game mainly lacked boarding.
Overall Moo2 had most of the thigns you would expect and more. It had fighters, tractors, beam weapons, projectile weapons, missles, energy missles, assualt shuttles(boarding), transporters(boarding), shields (with shield arcs), engine damage, self destruct, armor, other kinds of system damage, captins and crews, and bombs to mention the few. Plus a bunch of stuff you might not expect. Makes for very complex space battle, thou not most visually appealing. It is still ok graphically for its functionality.
As far as Battlestar, I dotn want to mix tv into it. But the new one has space combat very simular to Space: Above and Beyond. Where there are no shields, and there's a lot of pilot twitch involved.