"Epiphanies" is the first episode to make it clear that the Earth Alliance under President Clark is becoming afraid of Babylon 5. This isn't surprising given how (as one viewer noted) Babylon 5 managed to drive the EA's God-like allies out of the Milky Way Galaxy. You just knew that "The Illusion of Truth" was going to end up with an unsubtle hack job done on B5 by ISN. The more subtle plays elsewhere by the Earth Alliance were more interesting. Bester is brilliant and rather Amon Goethe-like Bester, complete with his love for the PsiCorps concentration camp inmate he seduced with better rations and housing. Developments on Mars are also interesting--Earth has done a pretty bad job of colonizing other worlds if, after so short a colonial period, the inhabitants are so alienated.
"Atonements" is also worthy for its take on a Minbari civilization that is fragmenting and doesn't deal well with change. Before she left Babylon 5, she told Sheridan that the Minbari have a ritual for everything, all the better to manage things. This can work well when the events involved are predictable. When they aren't, well, there's Delenn's reaction to the death of Dukhat: "He was the best of us. They struck without provocation. There was no reason! Animals! Brutal! They deserve no mercy. Strike them down! Follow them to their base and . . . and kill them, all of them. All of them! No mercy!"
We just know that Garibaldi is going to go bad. It's almost fun to watch, like Joss Whedon's pain-fed candy.