I would have rather more of the Maquis behave a little more than pre-betrayal Seska. After Learning Curve every single Maquis seemed more than happy to conform to Starfleet regulations. There shouldn't have been an outright rebellion, though maybe it should have come a little closer to that.
Like, maybe there are three or four Maquis constantly in the brig on minor charges, and they start to feel specifically targeted. Maybe a Maquis crewmember dies where Starfleet idealism causes Janeway to go into a trap, and Chakotay starts to fight Janeway on the philosophical appraoch for more than five minutes and doesn't cave in.
I would have ended that episode by Chakotay stopping a Maquis plot to assassinate Janeway, then Janeway making some concessions on 'regulation' behavior.
IMO Kes was a good character but for her to be really interesting they had to take her in darker directions than the network would have allowed them to. I like the idea of having a pure civilian character who was just discovering the universe with innocent eyes, but has all these scary abilities about her to discover.
They nudged against those themes in Cold Fire, then dropped them completely until instantly making her a telepathy Goddess to write her out.