On a purely technical level, B5's CGI has been eclipsed by a country mile. But I agree with the OP in that there is something I always saw in the CGI that I have yet to properly see in recent games. It can likely be brought down to a lot of things that have already been said, what with lighting and shadows, increased AA, etc. Basically things that don't get put into regular gameplay because most of the time you aren't in a choreographed cutscene, which is essentially what B5's CGI was.
B5 did very well, though, at portraying a sense of scale. Large cruisers FELT like large cruisers, even if technical details of the modeling and CGI fell apart when viewed under a magnifying glass. With most modern space games, it feels like I'm looking at tiny plastic models rather than actual ships of war. The Star Citizen trailer posted earlier is a pretty good example of that for me, something about it seems too neat and clean.
B5 also tended to spend less of its attention on space scenes, barring the large battles where choreography made up for everything else. When it's a flash in the pan as a companion to the actual meat of the story, you tend to be more forgiving.