The loss of O'Hare and his character seems to have upset the story arc quite a bit and introducing a new B5 commander rather than a new actor seems to have been a mistake in my mind.
Then I suggest you do some reading around. Michael O'Hare was (already) then battling mental health and other issues, which effectively forced JMS' hand in replacing him with Bruce Boxleitner. It was this that was one of the underlying reasons behind the whole Sinclair story arc that went on through seasons 2 and 3, culminating in "War Without End". And also the reason why the Rangers (and the white star fleet) started and then continued under Human command.
You also forget that it was the Minbari warrior caste that was anti-human and not the Minbari as a whole. After the events of "Moments of Transition", the political balance on Minbar changes, and the warrior caste lose a lot of their influence. Sorry, am geeky on the whole Minbari politics thing (I've done a LOT of research on this), as I'm in the middle of writing a fanfic that traces the events on Minbar from Grey 17 is Missing through to Moments of Transition as seen (mainly) from Neroon's perspective.
Also, there is quite a bit of material online which proves that JMS had to think on his feet regarding all the changes that he had to make: Michael O'Hare's departure from the series, other actor & character changes (Na'toth, Warren Keffer, Talia Winters, Ivanova...), the problems with WB etc etc etc. Effectively, what was produced was somewhat different to what was the original story arc.
Overall, I do think it stands up well. For me, it are the individual characters' journeys that really make the series for me - in particular, Neroon, G'kar, Londo and Vir. That, all the political machinations and for me, the sheer quality of the writing. How can anyone sit through G'kar's closing monologue in "Z'ha'dum" and NOT be moved?
B5 is not without it's faults, but it's still a lot better than much newer stuff out there.