Yeah, Freespace 2 is pretty much what he's saying he doesn't want, although the scale of the ships and distances involved are pretty significant. Xclusive, have you tried Freelancer? You'll still use jump gates when jumping between star systems, but within the systems, the playing field is vast and filled with a lot of nebulae, asteroid belts, junk fields, moons and planets etc. Using your cruise engines (prolly equivalent to Trek's full impulse) some of the systems can take 10-15 minutes to cross.
Otherwise, something like Eve would be closer to what you're looking for. The scale in that is truly immense! But everything takes place in real time, so it can take days to get to places. The only issue with it is that there can be a steep learning curve with Eve Online...