Okay, I'll play, too.
Sisko vs Janeway: As talented as Mulgrew is, I still have to give it to Sisko. (And Avery Brooks is a strong actor, anyway.) Of all the franchise captains, he was the most layered and grew the most. I tried to not let my bias of him being my favorite not get in the way, but even without bias, on paper he experienced the most growth and change, plus he was consistent. Janeway was far too uneven... a fault of the writers, not her.
Kira vs Chakotay: Kira wins. This is even a question?
O'Brien vs B'Elanna: O'Brien is my favorite engineer (only slightly edges out Scotty), but B'Elanna wins because she got more growth. O'Brien had the same advantage as Worf, just on a smaller scale. B'Elanna had to start from scratch.
Odo vs Tuvok: Possibly the most even matchup due to their role and both actors' abilities and talent. But I have to give it to Odo because he had quite a character journey.
Quark vs Neelix: Neelix is severely underrated, and was underutilized. Quark deserves far more credit than being the comic relief, because Shimerman brought a LOT of depth and nuance to Quark. Both actors really were fantastic in their roles and both characters served their functions well, but Quark wins overall because I feel his journey was more turbulent.
Bashir vs The Doctor: I feel Bashir is a better doctor, but The Doctor wins here because he was literally a blank slate when the series began. Due in large part to Robert Picardo, The Doctor is simply unforgettable.
Jadzia vs Kim: Jadzia wins. Kim was pretty static for the entire series, while Jadzia had good growth in 6 years.
Worf vs Seven: This is actually tougher than it appears. I think I will give the win to Seven, simply because she only had 4 years of episodes to grow in, while Worf had 11.
Ezri vs Kes: Kes had more potential, but Ezri wins because not only did the writers give her more attention in 1 year than Kes got in 3, but DeBoer is a stronger actress than Lien.
Jake vs Paris: I find myself surprised at how difficult it is to choose between these two. We literally watch Jake grow up, and he was just a regular person who carved his own path that was not Starfleet, like his dad. Paris had a great redemption arc, earning respect among the crew, and finding love and getting married and becoming a dad in the finale. I will give this one to Jake, because ALL the scenes between him and Ben were just special.
Total wins...
DS9: 7 (Sisko, Kira, Quark, Odo, Jadzia, Ezri, Jake)
VGR: 3 (The Doctor, Seven, B'Elanna)
As for secondary/recurring characters, DS9 completely outshines ALL other shows. There is simply no contest there.
