Berman wanted a maquis/federation conflict to be a regular theme on Voyager!?
Assuming that's true, I think there have been a lot of fans who are blaming Berman for things he never did. People have often complain that after the first episode of Voyager, there were only a couple of reminders that this ship had two separate crews who were former enemies. I've often said one season of Chakotay as captain after a mutiny, would have been awesome, and would have kept the audience in suspense of whether there would be another mutiny or not.
The great thing about the premise of Voyager is that they faced a different type of threat than the dominion or the borg presented, they faced the fear of the internal enemy; the two crews threatening to take and retake the ship.
Or at least that could have been what Voyager offered had they gone any where with it.
And now I hear Berman was in favor of the conflict? Wow.
And that just goes to backup my point that Producers do not have 100% control over the product they produce.
It's my understanding that the Network has more control than the producer.
A lot of the problems Voyager had, which Berman and Braga are frequently blamed for, were in fact UPN's fault. The best example is Year of Hell, which Braga originally pitched as a season long arc which would have lasting consequences for the series. Berman gave the idea his approval, but then UPN stepped in and said the story could be no longer than a two-parter, and had to be reset at the end.
I've never understood the series attitude of "it musn't contain long running arcs, networks might want to repeat the show out of order, etc etc"
Maybe it's just a British thing but we've had many different channels get their hands on Trek rights, from the 90s up until now, some with different levels of professionalism and commitment to others, and yet ALL of them have still started at season 1 and worked through them all in order.
They might pause a week or two for a sporting commitment or something else of that nature, but they always picked up next week right where they left off.
The only time I can ever remember the order being different is when Voyager was ending, Sky did a fan poll top ten episode rundown in the week before the finale, which meant they used up the rights to those episodes so in the next repeat run they missed out those eps, but once they reset themselves again it was back to normal.
Is this just a UK thing?
Re-runs in North America are almost in order, and at times when best of marathons are done it's not uncommon for those episodes to be omitted from the re-run line-up like you mentioned.
Although there are also examples of channels sometimes doing marathons, like what TNN/Spike did with TNG ten years ago. Basically, they did seven hour marathons every weekend which showed random episodes that had no real connection to each other. Even then, there was still some order, eg they'd start with a season 1 episode and end with a season 7.