For me, the maquis element was underused and eventually became irelevant - it was too quickly resloved and if you didn't start watching Voyager until season 2, you'd probably never even know there was such an element
I would have had the maquis maintain a genuine distance from the main crew and eventually would have had a season long arc that detailed a mutiny, a possible mini-war (on board a la die hard) and ended with it with the maquis (and a number of star fleet crew) finding their own ship and going their own way home which would have also been part of the show - one episode on Voyager the next on the maquis ship
anyway, i just wish more had been made of the tension between the two groups
I would have had the maquis maintain a genuine distance from the main crew and eventually would have had a season long arc that detailed a mutiny, a possible mini-war (on board a la die hard) and ended with it with the maquis (and a number of star fleet crew) finding their own ship and going their own way home which would have also been part of the show - one episode on Voyager the next on the maquis ship
anyway, i just wish more had been made of the tension between the two groups