I am currently re-watching the entire B5-series on dvd for the probably 10th time or so since the 1990s, so I can share some thoughts in this thread.
In answer to some of you examples, I didn't see Season One in the original timeline. LOL I started watching the show at the start of Season 2, but I had seen some of it so I knew what she looked like before, but not enough to have predictions.
So did I ! *LOL* I started watching B5 season 2 on tv. But I soon caught up with what was what (and then watched season 1 later).
I made all KINDS of predictions after the fall at Z'Ha'Dum, but none of them included the introduction of The First One. LOL I remember thinking he was going to fall into something that somehow caught him. The fact that he was told to jump meant jumping was safe so that couldn't mean he was dead.
I did not either predict that he would be saved by The First One. I too thought he would be caught by some kind of net, alternatively that Kosh/Vorlons somehow would aid him. I still didn't feel confident he would survive but at the same time it seemed kinda drastic to write him out of the series.
I would say I was disappointed in the Shadow War ending, but only with how quickly it seemed to wrap up. I didn't mind the method used, but I would have liked to see things stretched out to more episodes, but that is true for all aspects of B5. I think I predicted that somehow the Vorlons would come to their senses and stop fighting anyone who wasn't a Shadow.
I was a little disappointed by this too, how quickly the war ended. After the heavy build-up I think the war/heads-on conflict could have lasted longer. My prediction at the time was that the Vorlons would join up with Sheridan and his 'forces of Light' seeing the sense of cooperation to destroy the 'evil' Shadows. Not at all how it turned out, as we know.
Here are a couple of other items.
In ALL ALONE IN THE NIGHT, I thought Sheridan was going to be held captive longer than he was. I kind of wish he had been. That is an aspect of that episode I feel fell flat. They shouldn't have been able to wrap it up so quickly.
NEVER predicted Lennier's fate. Just didn't think things would happen that way. Same with Lyta.
At the time, in the 1990s, Sheridan was my favourite B5-character besides Delenn so it pained me a great deal to watch the episodes where he was captured, tortured and humiliated. I had never thought/predicted that would happen. I was therefore more than happy when it was all over and fairly quickly wrapped up. In the years since then, as I have grown older, though I still like Sheridan as a character I have come to appreciate the (subtleties of the) characters of G'kar and Londo more, and so I can better understand those who feel that that part with Sheridan was perhaps wrapped up a little too quickly.
As for Lennier, I never expected/predicted his betrayal of Sheridan either. It disappointed me at the time since I always liked Lennier's character in the story, but in retrospect I can see his 'dilemma' in that situation. What disappointed me most was that they did not give us some sort of resolution with regards to Lennier. I would have liked to have seen him return to Delenn and Sheridan after doing his 'penance' as a Ranger, apologize and gain redemption (but then again I am a sucker for happy endings.. *grin*)
Talking of predictions, I Never saw the Sinclair-Valen arc coming, that took me completely by surprise and I thought it was wonderful!