that was fun to read
Yeah when Star Trek Online came out I was wondering the same thing, what happened to the space flying games. It is not like we have had too many of them and it is not like we have never had great ones.
As you mentioned X3, but X3 tried to do too much and should have taken it down a few notches and just improve what they had and focus a bit more on making the combat and such more exciting and more fun.
One of my favorite space flying games though is Nexus Jupiter Incident, which if you have not played before you really have to play. The graphics in it are still good enough to blow your mind (which is shocking considering the game was released in 2004). The combat is both realistic, well shockingly realistic actually and at this time I will have to go right ahead and peg it as the most realistic space flying game to date. The combat was both hard, extremely strategic and fun and exciting. Though the game was held back by a large amount of bugs and a lack of proper advertising to get the name out there.
Nexus also had no side quests, no trading, just briefing, fleet set up and then directly to action filled with surprises and lots of great story. Unlike any other space game you never knew what to expect when entering the next mission, anything could happen often forcing you to redo a mission if you were caught off guard. One second you are scanning some derelict ship, the next you have a massive invasion on your hands. If that is not enough at times you will be greeted by enemy siege ships which unless you react fast enough (luckily the game had a pause mod to issue orders and what not) your entire fleet could be taken out within seconds.
Other than X3 and Nexus the only other great space game I can think of is Star Trek Bridge Commander, its bridge mode and direct ship control modes were both equally fun, each as usable and as effective as the other to play through the game.