I've been thinking about this, and came up with a few ideas.
First off, things should be condensed and streamlined. I enjoyed B5's 1 season = 1 year approach for that particular show, but let's be honest: did it really feel like an entire year had gone by each season? certainly not to me. So scrap it. Things take as long as they need to take, more like on BSG (season 1 covered like 6 weeks, they had time skips if need be, or several episodes can cover a single day).
Next, the story and characters we eventually got are iconic. I know there are people who would love to see the show as originally intended (including me, but not for an actual reboot, more like if I traveled to an alternate universe one of the first things I'd do is buy the dvds of the original 5-year arc), but to me it just wouldn't be B5 without Sheridan, Ivanova, and others. So I would do something similar to the actual show, but with nods to the original storyline, and streamlined to make things less awkward, such as:
This first arc covers several episodes - Ambassadors arrive on Babylon 5. Midseason or so, Kosh is attacked, and Commander Sinclair is framed for it. The Agamemnon, led by Sheridan and Ivanova (who had previously shown up in the first episode at the very least), is dispatched to investigate. They and Garibaldi uncover a conspiracy within the EA government, including first officer Takashima. They can’t go public with their findings yet, so Sinclair has to go into hiding, first rooming with Garibaldi, then being granted asylum on Minbar, where he begins his Ranger training alongside Marcus. Takashima is reassigned by her unknown masters and becomes a recurring adversary (perhaps involved with the Night Watch?). Sheridan and Ivanova transfer to B5 to fill the power vacuum (perhaps there’s a battle in which the Agamemnon is destroyed?).
Alternately, Ivanova could be B5’s second officer and only Sheridan transfers, leaving the Agamemnon in the command of his XO, Elizabeth Lochley.
Sinclair continues to be a major character on the show even after he leaves the station. He slowly learns about the hole in his mind, and about the coming war against the Shadows. He, Sheridan, Delenn, and Kosh have their secret Army of Light conspiracy going from relatively early on.
Lyta Alexander has a second personality, “Talia,” programmed into her by the Psi Corps. However it ends up going, she takes the super-telepath storyline of the original series, while Ivanova takes the political telepath rebellion storyline (though hopefully without Byron).
Also, I like the idea of Minbari being androgynous, with Delenn being played by a woman, dubbed by a man, and becoming female after becoming half-human. Let’s go with that.
What do people think of this?