I have a few more match-ups...
PRIMARY VILLAINS: Dukat vs. Borg Queen - While the Queen is a decent enough primary antagonist, she doesn't have either the duration of presence or story arc of Dukat.
SECONDARY VILLAINS - Weyoun vs. ??? The next best choice for a recurring bad guy on Voyager is either Seska (who got crunched by Garak) or that Kazon guy she took up with. Weyoun beats either. And even if you disqualify Weyoun because he's technically five characters, I think tertiary antagonist Kai Winn would compare favorably as well.
TURNCOATS: Eddington vs. Jonas - Eddington was actually an ally for a time, and followed more of an arc. The most interesting part of Jonas's story actually involved Tom.
MOMS: Keiko vs. Samantha Wildman - Ensign Wildman had some good moments, but Keiko was the more developed character.
ROMANCES: Worf/Dax vs. Tom/B'Elanna - Both were pretty decent, but having Jadzia die after she and Worf were together for so short a time was just... urghhh. The Voyager duo takes it.
KIDS: Molly O'Brien vs. Naomi Wildman - Hana Hatae was incredibly cute, but Voyager just did more with Naomi.
SILENT CHARACTERS: Morn vs. Ayala - Morn got his own episode. Plus, the fact that he never shut up offscreen was a pretty good joke.
COMPUTERS: Majel Barrett vs. Majel Barrett - For some reason, this one's a tie game.
Running score:
DS9 - 12
VOY - 4
Draw - 3