It's hard to imagine that anyone who was satisfied by DS9's overall story arc could feel satisfied by Babylon 5. For example, if DS9's treatment of the Prophets seemed fitting, then Babylon 5's treatment of the Vorlons must seem outrageous. Or, if the human role in galactic affairs seems appropriate to human stature in DS9, then Babylon 5 must seem like some kind of self-flagellation. If Section 31 on DS9 seemed so cool, then Nightwatch on Babylon 5 must be some sort of maniacal leftwing caricature. If Sisko's apoetheosis in the cave of Mt. Doom seems like a satisfying climax, then Severed Dreams must be a nightmare.
You're kidding, aren't you?
The Prophets on DS9 were interesting in concept and in the beginnig also in execution, but in the end disolved into a very simplistic good vs. evil thread, while the <REDACTED> vs. <REDACTED> conflict on B5 initialy seemed to be a simple good vs. evil story which then morphed into something much more complex and interesting.
Sec.31 and the Nightwatch can't even be really compared, the Nightwatch is not presented as an secret organisation that operates above the law as Sec.31 is. Also i'm pretty sure that Sec.31 is not supposed to be cool and that the audience should have the same aversion, that Bashir feels.
Sisko becoming one of the Prophets was a good idea but the way it happened was very unsatisfying (as the Prophets storyline had long since fallen apart), while Severed Dreams
(where i fail to see any comparability to Sisko's apotheosis) might be one of the best episodes of american sci-fi television.