I love the Voyager concept, mainly because I always thought it was like
Homer's Odyssey in space. But, in reality, it didn't really work out that way because of the "creative" producers.
For example, an episode where the crew are thinking of just colonizing a planet, or losing their identity as Alpha Quadrant residents (Starfleet or Maquis), which was a theme in the Odyssey as seen in the lotus-eaters.
Story arcs in the series. More moral issues, such as breaking the Prime Directive. Maquis retaining their uniforms for at least the first three seasons.
A big one would be to keep Ron Moore on the production team (and get rid of Braga). He had some great ideas for the show, but they clashed with Braga's ideas. With Moore, the show would have become more realistic, more gritty and more dirty. For instance, an episode similar to BSG's episode "33" where Voyager has to keep running away from the Borg for days, and how it strains the crew mentally and physically. And the ship would not magically look brand new every episode.
(However, it could probably butterfly away BSG-2003
)
Also, don't have Voyager defeat the Borg almost every week. Keep them scary and unstoppable. They were the ultimate villain until Voyager got their hands into them.