Perhaps another way to look at it: who should have been Voyager's Miles O'Brien? I think I've suggested elsewhere that Eddington could have filled that role. He was a minor character that played the role of the antagonist well. Perhaps more importantly, he was the one person who did not just see the Maquis as a protest, but as a way of life: an actual counterpoint to Federation sensibilities. Chakotay, whatever his leadership ability was, largely believed in Federation values (at least to the extent that his heritage allowed). Eddington as security officer (give poor Tuvok a promotion, he's an old Vulcan) would have done more to sharpen differences of outlook on Voyager.