Even the rebellion of Babylon 5 itself temporarily creates two human polities but by the end of the run there's only one again. It is apparently inconceivable to both the rebels, the shadow backed human government and the writers that there could be two independent human governments. The civil war among the Minbari follows the same pattern.
More problematic for me were the Shadows and the Vorlons. Clearly for dramatic purposes one wants to have two strong opponents with different philosophies. However, what is the need to make these two distinct species? Then there is the Shadows and Vorlons leaving the galaxy. What, all of them? Every single one? Regardless of how attractive exploration of such a new environment would be, it's extremely difficult for me to believe that every individual of entire races would as one pack up and move.
I don't want to pick on Babylon 5 in particular. I liked it very much (at least seasons 1-4). This kind of tribalism is endemic to space oriented science fiction. Just consider the Star Trek universe (the Star Wars universe doesn't because only humans matter there). I suppose it's easier in terms of dramatic structure and story telling because then the racial designation becomes a convenient short hand. But I wonder if it doesn't demonstrate something avatistic in all of us, that even forward thinkers still postulate an essentialist and tribalist future once we get off this planet.
UPDATE: Orrin Judd has a post that is very apropos to this one. The key part is his review of John Gray talking about the European Union project. This is a very Babylon 5 view of the future - an organization that is democratic among the tribes with the presumption that each tribe/nation/culture/race/species is unitary and that all that is required is to adjudicate among them.