[Baron Munchausen]

First and foremost for Babylon 5 is the jump gate as the means for getting around the universe rather than the warp drive. It's too bad MM never made the relatively small changes to the SE IV code that could have allowed technological warp points along with the 'natural' ones. A parallel hyperspace for ships to travel in would also not have been too difficult to do. Since the hard code is not designed for this method of movement, it's rather difficult to mod in.

After that, B5 seems to be different from the typical "pop culture" scifi universe in the survival of religious beliefs. Usually, scifi is either a-religious or outright hostile. Star Trek is rather famous in this regard, because of so many episodes depicting dead-end fanatical cults, and hardly any prior to DS9 depicting a relatively balanced and continuing religious tradition.

Depicting this in the game is also difficult. The various 'culture' effects possible under SE V would be much more useful in this regard.

The only thing I think you could do to make the SE series more like the B5 universe would be to eliminate shields and place all defense emphasis on armor and ECM/countermeasures. This would make space combat between all but the most evenly matched forces rather like air combat today -- short and sharp. (And thus, the emphasis of the game would end up on politics rather than military strategy.)