I'm in line with those who felt the conclusion was disappointing. Not because it didn't all end in a one big space battle but because it just didn't manage to convince me. I simply didn't buy that the Vorlons and the Shadows would leave like that.
The more I think about it, the more I think it's probably the execution that bothers me (as well as others, it seems). The idea itself is very interesting and works for me on paper - just not on screen.
I think this is largely due to the fact that I find Boxleitner and (even more so) Furlan pretty weak as actors. And to pull off something like this you'd really need somebody like Peter Jurasik or Andreas Katsulas (if you're looking at B5 itself) or Edward James Olmos, Mary McDonnell, Patrick Stewart, or Andrew Robinson, to name a few examples of actors from other shows.
I honestly think that the production problems really aren't important at all. Yes, the help provide understanding for the makers and why things might not have turned out the way they wanted but, in the end, all that really ever counts is what's on screen.