Well for one, I think the effects on Earth because of the Minbari/Earth war would have been more profound. I can see the Battle of the Line becoming the Battle for Earth, with the war ending after major cities are wiped out and only a fraction of humanity survived.
Thus the point of Earth being involved in the Babylon Project would not be to secure the peace, but rather to seek aid from the other worlds to survive.
I also think the First Ones (including the Vorlons and Shadows) would have acted more from the sidelines, maybe not even fully revealing themselves, rather acting through the younger races. Similar to the "Head Six/Head Baltar," characters like Sheriden, Delenn, and Sinclair who were among those closest to Kosh would be prompted to do thing by a proxy for Kosh. Likewise, Morden would be a "Head" character for Londo.
's attempts at humor would all be erased. I know some who would probably welcome that!
Also, more characters would have had sex and with multiple partners. When you think about it, the characters in B5
were mostly monogamous. Not so much in BSG
, at least where Kara and Lee are concerned.