Voyager had some conceptual problems right from the start, and I really think they should've done what Berman wanted and wait until DS9 was done to do the show.
Other than that, the whole "Maquis should've been enemies longer" thing really isn't that much of a problem.
The problem with the Maquis was that the source of their conflict, the DMZ, was now 75 years away. The Maquis were the enemies of Cardassia, not the Federation, and whatever negative feelings they had for the Feds wasn't going to blind them to the fact that these were the only familiar folks around for decades. It wouldn't have been productive for the two crews to be that combative to one another the whole way through.
And even if they were, the tensions would've died down after 1-2 years. If they kept it up after that, then they had to have serious mental issues and they'd likely never get home.
What the show needed was another plot to drive the stories beyond "Going home" which could never be accomplished because...the show would be over.