So. Volume 15 of the Babylon 5 script books just came out, and according to the blurb on the page linked above, it includes
BREAKDOWN OF THE ENTIRE 5-YEAR STORY ARC WITH SINCLAIR
"For over ten years, fans have asked 'What would Babylon 5 have been like had Sinclair stayed?' After we finished the movie, but before we got the series going, WB asked to see a breakdown on this five-year arc thingie. So I wrote a six or seven page, single spaced outline of the entire five years with Sinclair still in place. The document makes for fascinating reading when compared with the series as it developed. Not only that, but the same document has a brief outline for A POTENTIAL BABYLON 5 SEQUEL SERIES, which would have been entitled BABYLON PRIME."
The arc document is insanely different from what actually happened on B5. This is true even for Season 1, and JMS claims in his introduction to it that he wrote it at the beginning of Season 1 (i.e. after "The Gathering").
If you'd rather read this on your own, or just don't want to know, don't read any further, to save yourself from alternate-world B5 spoilers!
The only Big Events that survived basically unchanged are (a) B4 reappearing for a few hours (i.e. "Babylon Squared"); (b) Delenn turning human and getting involved with Sinclair (not Sheridan, who doesn't exist here); and (c) Kosh revealing himself (all angel-ly) to save Sinclair (who is falling from the core shuttle) at the end of Season 2.
The entire Vorlon/Shadow conflict looks different. The flip-side of "Babylon Squared" (what we know as "War Without End") is listed as happening in "Babylon Prime" — the sequel series — and Babylon 4 would be timeshifted to the future, not the past. Some of the plot points that did survive occur much later — it looks like the original arc only covered through what happened in Season 3 or a bit of Season 4 of B5 as it aired. It ends totally differently (and seriously downbeat). There's no "Sleeping in Light" 20-years-later equivalent.
Sinclair's girlfriend/fiancee, Catherine Sakai, does not end up going to Z'ha'dum, as I expected (I had only recently realized that she would have been the equivalent of Anna Sheridan, which is a bit of a "duhh" moment for me; I'm slow) — instead, she gets mind-wiped in some vague fashion (not linked to the Shadows). The Shadows don't get revealed, according to this memo, until Season 4. Season 5 includes the Minbari warrior caste restarting the Earth-Minbari war, and destroying B5 at the end of the season. The end of the season and the series sees Delenn and Sinclair, with their love-child in tow, on the run from basically everyone, including Earth.
Then the memo goes into a "Babylon Prime" sequel series, which includes stealing Babylon 4 (which is actually a space cruiser as well as a station, which makes little sense to me), what looks like the Shadow War, and a bunch of other stuff, some of which echoes what ended up in the B5 series.
I actually thought (and maybe still think) that this memo was a joke, it's so insanely different from the show that aired.
Actually — it's not so much the differences per se — it's more how JMS always seemed to imply that he knew exactly how things were going to go, and that they didn't change that much.
On GEnie, 11 April 1992:
A few days ago, I sat down with our line producer, John Copeland, and production designer John Iacovelli, and we were talking about the need to move quickly on some stuff, and how painful the process is to have the whole story in your head, already told, really, and then have to make it all over again so we can put it on film. "You think you've got it bad," I noted, "I've already worked out the last scene in the last episode of the last season (#5)...and I've still got to make Movie #1." They called me on it and asked what that scene was. Just to see their reaction, I told them. They looked at me as if I'd suddenly sprouted three heads and feathers. It was worth it. (Happily, they're sworn to secrecy.) It was also good because I think that, even without filling in the beats in between, it gave them a good sense of where the series was going to go.
— according to the "arc memo", the end (of the sequel series) is Sinclair fishing quietly on some uninhabited world. Which doesn't seem all that interesting, really.
And then there's this other quote from the Lurker's Guide page for "Sleeping in Light":
"What this boils down to is... is the ending you envisioned at the start of Babylon 5 the same today as it was then?" For the most part, yeah...it's gotten a bit refined over time, the way it always does the closer you get to it...it's like seeing a mountain from a great distance, then closing in until you can make out the details. But basically, yeah.
Which means that either JMS is way more flexible, mentally, than I ever knew, or he's just put a huge one over on us. I guess we'll see.