Voyager in particular always saddened me, as I felt it should have been the first Trek show to start out completely serialized. The conflict between Janeway and Chakotay would have been ripe. You could even have members of the starfleet crew consider joining the Maquis. I would have had Janeway be the XO initially, and have the CAPTAIN die. Before leaving Starfleet Chakotay would have been a commander, and that way the two would be butting heads over who should really be running things. They harmonized the situation way too fast in the pitifully small number of episodes dealing with all that.
There are many other layers to consider there too. The acquisition and decline of resources, some members of the crew literally losing their mental stability from being so far from home.
Instead of Neelix, I would have had some of the Maquis fill in his role, being as they were all about fighting for survival and such they would be invaluable and coming up with new ways to feed the crew, and deal with the hostile threats of the delta quadrant in new and interesting ways. There's many other things that they could have done to really use what they had, and make the show about something. In this case, two different methodologies, and ideologies forced to come together, and the resulting conflicts and harmonies that would arise in having to make do with a pants-fillingly dangerous and unknown corner of the galaxy. An ongoing struggle, nothing pat or easy. No reset button.
That's radical. I like it.
My redesign of Voyager would have been somewhat more radical. For me, "Caretaker" should have been the first season cliffhanger/finale. In the first season, Voyager would be essentially TNG-lite in the Alpha Quadrant, though with the ship pursuing Chakotay's Maquis cell and coming into conflict with him from time to time. Essentially, we would get to meet the characters who die in "Caretaker" (maybe the helmsman and the XO get their special spotlight episodes), while Chakotay and his crew are a recurring villain throughout the first season. Then, at the season finale, half of the main cast is killed and Janeway is forced to ally with characters who have been portrayed as the antagonists all season long.