I've read most of this thread, and found some of the discussions quite interesting. I neither hate nor love Voyager unlike some, I think some people need to realise that there where a lot of things the producers were not allowed to do back then.
The thing is, VOY did have the best premise of the Trek shows, however in order to do it justice they would have needed to approach every aspect of the show very differently. They wanted 26 standalone stories per season, and that alone killed 90% of the potential, given this restriction they did a good job. For what it's worth here are my random thoughts;
*As external conflicts would have always been difficult to develop, internal drama should have been a priority. I personally would have had a massive amount of Voyager personnel killed in the pilot, meaning most of the qualified and elite crew are gone. I'd probably have done something like this for the crew;
- Janeway- 1st officer of Voyager, takes command after death of Captain. From a science background, not as much leadership experience as other Trek captains, takes failure really badly and doesn't have absolute confidence in herself, utterly determined.
- Maquis Captain- Grudgingly accepts 1st officer role despite having more experience than Janeway. Early in the show considers mutiny, possibly even attempts it, realises that he doesn't have the crew to staff Voyager and as such is forced to comply
- Cardassian Crewmember- A high ranking military officer captured by the Maquis and held aboard the Maquis ship. Beaten and interrogated on a daily basis for information prior to the Maquis being stranded in the DQ. Initially put in the brig aboard Voy for his own protection. Voyager's Ops Officer was killed in the pilot, Kim has been manning the post but doesn't have the experience to do it and the ship suffers as a result, in the absence of other qualified personnel Janeway allows the Cardassian to take the position, and tutor Kim, over the complete objection of all serving Maquis. Having spent years coordinating Cardassian personnel he does an outstanding job but is a source of conflict.
-EMH- Similar but make his desire for equality a bit more subtle and no mobile emitter. If the crew consider abandoning ship it means abandoning the Dr.
- Kes- Stick with the concept and don't get rid of her! Have her very immature early on, show her desire for a normal life through the early seasons with Voyager crew disturbed a 3 year old is hitting on them etc. Have the show finish with her as an old woman, having lived her entire life parallel to this journey.
- No Neelix, or at least a massively different Neelix.
-As for other characters, either make them more interesting or change them.
It goes without saying the Maquis would have no desire to put on Starfleet uniforms. If that moment comes I'd expect something special to lead up to it
*As for damage/support/repairs etc- Obviously neither proposed extreme is ideal. What they had was ridiculous, the ship may have well been in the AQ. Having no repairs would mean the ship wouldn't be able to survive anything or go anywhere. I think if the hull is badly breached and there is visible damage, they need some kind of explanation for it's repair (use of a friendly alien shipyard for example). It would be great too if there could be some sign this had happened, different coloured panels on some sections for example. Internally, if the bridge is trashed in an episode, it would be better to have it be trashed in the next episode, looking slightly better each week as the debris is cleared and the walls are repainted etc. Even if this all happens in the background in 1 episode, it is better than magically regenerating. Have certain corridors be wrecked and fire damaged for an episode or 2 after big battle, the crew doesn't need to discuss it, just be a nice visual for when they are walking through discussing something else.
*Rationing and low resources should have led to some interesting moral debates. The possibilities here are endless.
*Holodeck shouldn't have been used at all
*Given that Voyager was alone and without the backing of the Federation, their treatment from hostiles should have been far more brutal. Even if an enemy has an advantage over Picard's Enterprise, they don't beam aboard and start executing his crew because they don't want to be at war with the Federation. There were opportunities for some intense scenes. I also hated the way Voyager/Janeway had to "win" at the end of each episode, it comes across like kids TV sometimes. Have Voyager threatened, attacked and narrowly escape with their tail between their legs, watching these proud strong characters have to deal with that is far more interesting to me than Janeway "taking out the garbage"
*On a related note, no Janeway/Borg Queen conflict. It literally became a Saturday morning cartoon. Surviving the journey, and trying to keep some cohesion within such a diverse crew would be far more compelling. Since external threats could never be that well developed (given that Voyager doesn't stop), then the antagonists should be looked at like The Walking Dead's zombies, they cause the problems that create the drama but are never going to be developed.
*Given the show was set to run 7 seasons, a change of pace from time to time might be good. For example if Voyager suffers massive engine damage, have them land on a planet for repairs, but due to the amount of damage that story could run 4 or 5 episodes, just think it through in advance and make the planet a particularly fascinating one and the story that's told there be something that really holds the audience interest.