Another problem is the thread of Babylon 5’s prophesied destruction, one of the few plot points that was very clearly a victim of the eventual changes in the storyline – the resolution in “War Without End” never felt particular satisfying, and has massive plot holes. Most of the time, the show does a pretty good job of clearing up abandoned plot threads in a satisfying fashion, but this one really sticks out on re-watching.

I've always thought the opposite really. We see what is essentially one of the very last scenes in the show early on, but it isn't exactly what we think it is.
I read the bit about the original ending, but the way it played out really fits togeather far better then what was billed to the network; I wonder how much was just sales pitch & spin off opportunities to get the show going.