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.
The thing is, though, people can like completely contradictory works of art. Liking DS9's treatment of the Prophets (which I didn't, BTW) doesn't necessarily mean that person would think the treatment of Vorlons was outrageous; they're different shows with different ideals, even if they do have stuff in common. Batman is Batman, but I'm able to enjoy both the Dick Sprang, bright and colorful, Robin-with-no-pants era Batman and the Frank Miller, hidden in the shadows, breaking people's arms Batman. Liking a particular work of art does not preclude one from liking a work of art that goes in a different direction.
Interesting, BTW, that you chose Severed Dreams as B5's equivalent of "Sisko going into the cave of Mt. Doom;" surely that'd be Z'ha'dum?