I've said it before - what could've been cool is if the renegade Maquis were the CO of Voyager and the idealistic first officer was forced to follow him/her. Voyager gets stranded, her original CO gets killed, but not before putting the Maquis commander (as the most experienced officer, etc.) in charge. DIdn't mind what we've got, but there's no better way of putting an intra-crew conflict together but to have the lead character having to fight it every day.
That would've been interesting. Part of the problem was, Chakotay, who was the Maquis lead, spent most of the series being Janeway's yes-man. So naturally it only followed that the rest of the off screen Maquis were being brushed aside, used only for cleaning plasma conduits and building shuttles. If he behaved like he did during Caretaker the whole run, he might've been able to pull that off.