But I don't think he ever challenged her anymore than any starfleet officers did their captains. First season Kira challenged Sisko more. I wanted some drama on the level of Lily and Picard in FC. Chakotay wasn't enough of a free thinker to me. His personality was definitely never explored as well in the show as it is in the books. I feel like I didn't get to know Chakotay as an individual until the relaunch.
Both Lily and Kira were not Starfleet officers. Kira only became one for a specific mission to Cardassia in season 7 of DS9, and then officially in the relaunch. Lily was from 21st century Earth...
But I do agree that the Kirsten's relaunch has been amazing for Captain Chakotay and his personality