Of all Star Wars games I know about, none seem to be specifically about capital ship-vs-capital ship combat where you captain a capital ship in an attempt to defeat other capital ships and space stations (much like Starfleet Command I-III or Bridge Commander if you ever played those games) where one can capture other ships, target a ship subsystem, boost sensors or shields, and in SFC3, microjumps. I wonder why there seems to be no such Star Wars games... but also what kind of player wouldn't want to captain Star Destroyers (if you're a classical trilogy fan) or Droid Control Ships (if you're more of a prequel buff) in combat? Even the closest equivalents (Empire at War) seem to have both a ground component and a space component and, while the space component does feature craft each with their own strengths and weaknesses, it does not feature the level of detail in how a captain can control a capital ship that the SFC series does. I understand that Star Wars lore seems to be more small craft-based than capital ship-based, however, in the sense that the major canon characters seem to mostly fight in fighters or other small craft (Millenium Falcon being the best-known example) than capital ships - it seems that capital ships play more of a supporting role in SW lore (or at least those without superweapons mounted on them), despite their importance in space combat.
There are mods out there for Bridge Commander that lets you duke it out capital-to-capital ship in terms of Star Wars ships (and other media too). I do agree with your points though, there really isn't a traditional game molded around that principle of capital ship versus capital ship. I mean you get the X-Wing series of games, but that's just fighters. In X-Wing Alliance you could mod the ship list to fly like Super Star Destroyers and what not, but it's only flying and no other commands like launching fighters or whatever. I think a capital ship to capital ship game would also need tactical components too like an RTS to help balance it out as well..
That's what I liked most about SFC1-2: there were numerous tactical components. Launching fighters, ECM, shield management, boarding action being the main ones. The closest thing to playing it like a Star Wars capital ship captain would be playing as the Hydrans: compared to most SFC1-2 factions, which include four canonical Star Trek factions, Hydrans are the ones that rely most on carriers - they seem to operate capital ships much in the way Star Wars factions operate capital ships, assuming, that is, that capital ships are ships frigate-sized and up.
If you want something more in depth than Empire at War the only thing I can really think of is Sins of a Solar Empire: Rebellion and it's Star Wars mods. http://www.moddb.com/mods/sins-of-a-galactic-empire http://www.moddb.com/mods/star-wars-interregnum http://www.moddb.com/mods/star-wars-ascendancy
