I have not played x3 but it seems to me that this one is more story driven through a series of missions. If x3 is an elder scrolls where you mostly can wander around and do exploration, then this one is probably a mass effect, where you follow the story and evolve through it.
Also, as much as it might be a RTS, I find it so atypical that I have difficulties to define it. You mostly command your own ship, sometimes alone, sometimes part of a fleet. Sometimes you also have the possibility to have other ships at your orders though, but it is mostly focused on tactical choices revolving around your ship with a lot of interesting little mechanisms like passive/active scanners, different kind of weapons, a very complete way of "fitting your ship", boarding other ships, etc.