Like I said, the Maquis were kind of a not-well-thought out idea to begin with.
I disagree. Preemptive Strike on TNG and practically every Maquis episode on DS9 were gold, IMO. What made the Maquis so great was that they were sympathetic characters with admirable goals, but unlike Starfleet they weren't bound by rules and restrictions, or for that matter even their own conscious. Kind of like Sisko in In The Pale Moonlight. They'd do almost anything in order to accomplish their goals. The Maquis on Voyager should have been willing to stand up to Janeway and question her authority, and, if necessary, remove her from her position and put someone in command who was more likely to get them home faster and in one piece.