There are a few scenes in the original pilot that weren't included or were cut from "The Gathering". There was that "Privacy" part to the Leeta-G'Kar conversation, as well as the rest of that conversation after the "pleasure threshold" line. There was also a tiny line that Sinclair gave to Leeta as they left customs. He says that he's showing her to her quarters, then playing off her nature as a telepath, says that she "probably already knows where it is". That line was cut, probably because the whole altercation with the gunman at customs added for "The Gathering" took the light mood out of the scene, that would make that joke a bit out of place. Aside from other deleted scenes being added, or cut pieces being reinserted, graphical improvements, Kosh's "Entil'za Valen" line, and the audio overlay during Sinclair's recount of the Battle of the Line, I don't remember any other significant differences between the two versions.