A) Yes, DS9 did a better religious story than B5; but B5 blew them away with subtlety, politics and above all else, SPACE COMBAT! Which, honestly, is the only reason to watch science fiction. Without combat, isn’t it just basically a romance novel with no romance and no novel? :P
B) In regards to Janeway with the cubes and Kirk, Kirk took out the Klingon Empire. Not sure if that’s equivalent to a smattering of cubes, but I would have to say it’s gotta be at least as good if not better. Picard and Janeway together had to work on the Borg situation and even then, they had Klingons and Romulans. Janeway fought the Hirogen to a stand still but Sisko fought (fine, WORF fought!) the Dominion to a stand still. Of course, Sisko had a defunct old battle platform while Janeway had the top of the line science cruiser complete with abaltive hull armor. Meanwhile, poor Kirk is running around in a Constitution Class death trap being held together by spit, prayers and Scotty’s ingenuity!
I guess if it came down too it. I’d take the crew and captain of the Enterprise and Enterprise-A over that of the Enterprice-C and Enterprise-D or Voyager or heck, even the NX Class Enterprise for that matter. (Though, if you ask me, Archer was the cutest captain of the enterprise!)