Having the larger plot arc actually improves Babylon 5 because they have the long term character development built in - the alien ambassador who caused a war now healing the divide between species, Londo starting off as a nostalgic and ignored official to emperor (losing his freedom and nearly all he loves as he gains power), the telepath who starts as a loyal member of the corrupt Psi Corps to become the instrument of its destruction and liberation of the telepaths. Dr. Franklin who wants to build relationships with other species becomes the head of the medical division of Sheridan’s “Federation”.
Some of the minor character arcs are just as amazingly developed. The man who had his mind wiped as a punishment for murder and lives as a monk, wonders if he’d be as strong as Jesus at Gethsemene, gets murdered in retribution, and his murderer is sentenced to the same fate he had.
For a professed atheist I was always amazed at JMS’s sensitivity and respect for religious belief.
A lot more profound concepts being discussed than your run of the mill sci-fi programs. You are exactly right. This is what made this series head and shoulders above the more juvenile competition. It dealt with adult themes and philosophical issues, and it had a larger message than "the prime directive."
It also starkly contrasted "good vs evil" and then showed that sometimes what is good and what is evil is a matter of perception, and sometimes it is objective.
This was the first time I saw a complex larger plot arc in any science fiction series, and it was a breath of fresh air to me.
I hear there is still talk about making a movie, and I understand that J. Michael Straczynski has already said the character of "G'Kar" will be retired, and no longer appear in any subsequent movies or remakes. I still look forward to the possibility that we have not seen the last of Babylon 5.