I think the very love JMS had for the show is ultimately where the problem was with Season 5. Feeling that a Season 5 was uncertain, he packed too much into Season 4 in order to complete the story he wanted to tell.
Then with Season 5, it picks up very soon after. One possibility would have been to to kick the series forward by 18 years, starting with Sheridan's retirement from the IA. Introduce some new actors, but have the original actors in walk-ons (made up older) and flash backs (actor's normal age).
They could have introduced the story line of Crusade too. Maybe Londo visits Earth (finally reconciling?) meets Sheridan Junior, and then his Keeper sets off the plague.