Well, I liked X3, but not until I got rid of the starforce s**t it installs.
And yeah, I think you can command up to a whole entire fleet in it. Really steep learning curve though, which sucks when I decide not to play it for a long while and have to relearn everything.
SoaSE I havent tried yet, but from what I have heard and seen, it reminds me a lot of Nexus: The Jupiter incident.
Nexus: The jupiter incident Was a decent game IMO, but it did have its issues, mainly story/dialogue related. It was purely RTS style space combat though with some exploration aspects. The actual scale of the systems in game you fly through are definately impressive but it can take forever to get from point a to point b. Battles have plenty of eye candy. From being able to see and zoom in upon every individual detail of every ship, including fighters (to the point of even seeing tiny directional thrusters in use and docking bays on ships open and close, as well as the many turrets moving on capital and cruiser sized vessels among many other things. There are plenty of mods out there (Includeing a stargate one i am addicted to.) As for other stuff pertaining to combat it is very strategic, you can just focus on blowing up the main part of the ship itself (which will get you killed), to targetting individual subsystems of the space vessels and just leaving them completely disabled while you tear it apart or capture it for your own use. You can even assign officers to individual ships (on a capital class Ive had around 20 officers doing individual tasks such as sensors, med bay and whatnot.)
Then there is my favorite, which is freelancer.