I have to say, it's good to see a thread on this topic that is still (somewhat) active. Most of the time I find anyone discussing this sort of topic it's somewhat dated.
It is truly sad that proper space simulation games have, for the most part, fallen by the way-side, and I feel that it is largely due to the fact that today's audience are, as has been mentioned, looking for more instant gratification than something that is actually intellectually challenging. Big explosions, fast action, cool-looking pointy things - that's about as far as most people go.
I have been looking for a starship simulator for a long time as well, and have almost gotten to the point of giving up. I do have to say that I have rather high expectations, but given the capabilities of today's computer systems, I don't think it's too much to ask.
Games such as X2/X3 are great games, allowing you to branch out from the typical mission-based "I'm going to go kill some bad guys today, same as I did yesterday, and the day before (etc)", but as has been mentioned lacks the appropriate feel. Jump into a capital ship and it's basically like a painfully slow fighter. The point that (almost) made my day was the so-called Manual Ship Computer Interface (MCSI). When I first read about that, I almost fell over myself - a game that allows you to interact properly with the ship's computer? Brilliant!
Unfortunately, once I learned that it is more-or-less just a scripting console I was sorely disappointed. It allows you to script your vessel to act more as an AI, and in that regard it's great, but not what I was hoping for.
Universal Combat, however, deserves some more consideration. The concept as described by Derek Smart and 3000AD is actually quite impressive, particularly considering the capabilities of computers when he first came up with it. Even playing the game, I can see the concepts attempted; the main killer was the fact that it was a garage development with essentially no budget.
Independence War and I-War2: Edge of Chaos were both brilliant games in terms of the engine and implementation, but unfortunately for me the downside is the lack of interactivity - each action seems to be basically one-shot - fire and forget.
I was around on the Starshatter forums when it was in development, and even then it showed a lot of promise. Particularly given the fact that it also started as a garage development, the transition between concept and implementation as far as I can see is great. It is, however, focused more on tactical simulation rather than command of a single starship, so while a good game, it's still not quite what I was looking for.
The common fail-point for me with most of the games available is also the fact that they are generally arena-based. Space is supposed to be infinite in all directions. I understand the fact that creating such a universe is complicated, but it would be a vast improvement in my eyes - particularly the removal of the typical Gates, Wormholes, Single-System 'L-Points'. My idea is that you should be able to pick a direction and fly - you'll hit something eventually. Think Minecraft - procedurally generated starsystems, perhaps with a core of pre-defined systems. Oh, and people? SPACE IS THREE-DIMENSIONAL! All well and good to have 3D control in-game, but 2D navigation is unrealistic and, in my opinion, looks 80's-ish.
What I would like to see is something coming out that is a combination of each of these games: the complexity and openness of the X-series and the implementation of an actual ship computer, the (conceptualised) system control of Universal Combat as well as the multi-platform game play (from flying your ship to running around like a lunatic on the ground), also being able to walk around on your ship and interact if not with the crew then with the consoles, the relativistic distances and Newtonian physics of I-War2, and the tactical complexity of Starshatter.
Oh, and another thing that really bugs me: so many games say that you put your ship in orbit. Someone should really tell them that entering an orbit isn't as simple as flying nose-first towards a planet till you get close enough to be able to either transport to jump into a smaller ship, then giving your ship the Halt/Stop command. Space is not a road, and orbits are complex things. Think Orbiter - it isn't that hard to set up an orbit, and it gives you both a much greater sense of satisfaction and accomplishment and makes it feel so much more realistic. I'm not saying it needs to be as complex as in real life, but the implementation of an actual orbit around a planet would be a great step forward - think of the potential tactical implementations!
Seriously, how cool would it be park yourself in a mid-range orbit and take a stroll to the observation deck on your ship and pick out continents you want to visit on the planet below!
Like I said, high expectations, but I think it's within some sort of reason.
And yes, I understand that having a developer come up with both models and maps of ships is something of a tall order, but there is a massive community of people with extraordinary talent who could design and implement their own vessels with the right kind of modding system/API.