I wrote this a long time ago so it has changed over time.
Let's start with one simple change.
Instead of Voyager, make the Maquis ship be the one that survived.
Suddenly it's Janeway screaming for Chakotay's help and showing what a bumbling nincompoop she was.
Now if that's not possible, let's start with some basics.
1. Did anybody know where the ship was week after week. I didn't. There was no way to show how far they had to go, and what they had to travel to. A web page would have been a nice touch, and a descent map would have seriously help show how @#$#@$ the team was.
2. Make Chakotay the Robert E. Lee character he was supposed to be. Polite, charming, but completely ruthless when his family is at stake (take a page from Garek will ya).
3. Neelix should have been a true rogue, instead of our friendly martian. There was a TNG episode that had a true friendly rogue that they should have patterned Neelix off to add conflict to the crew (by trying to get into the uniform of every female member of the crew, and every so often succeeding)
4. Janeway could be left the same (If they won't follow my editing), but she should have died during mid season, passing the torch instead of always being the most incompetant member of the crew.
5. The Kazon were bad Klingons with afros. They should have looked totally different, and made more, tribal.
Also The Trabe should have been made more then an one episode wonder and became as much a threat to voyager as the Kazon were. Perhaps a little chamber music, while they systematically kidnap and experiment on many of the voyager's crew, altering them forever.
6. The ocompa could be written out without batting an eye. Kes was a concept that never quite worked. They should have made her age more drastically in the series, and when cut, should have keep getting revenge on the crew, instead of during a one hour episode.
7. Seska was a cool concept, but being put with the Kazon, just didn't work.
8. The Borg did not deserve to be pussy whipped!!! I can't believe after being in the best star trek two parter of all time (the best of both worlds), and the only next gen movie that didn't suck (first contact), they would destroy one of their best villains in the name of the worst ship in the federation.
9. A forum should have been setup to throw ideas and give input on what voyager had learned about the races. Races should have been as distinctive as that one race that collects organs to survive (never remember their name).
10. They should have spent a season away from the federation, but in the alpha quadrant. I was so looking to watching the voyager crew getting humbled by Garek (in charge of the Cardassian empire) or Martok and Worf.
Good chance to bring back some classic trek races like the Andorians and gorn, and put a new twist on the information to put some original story telling in place.
11. More of a mixture of low tech/high tech. Voyager seemed to be the love boat with virtually no scarse resources (except for that multi-parted episode), unless it was convenient for a plot device. Show them pulling true macgyvers and using low technology in ingenious way to compensate for their lack of resources. show that the federation education works beyond reversing the polarities, and make the ship feel grittier. Also have the ship go through serious appearance changes as they cannibalize their own technology and integrate alien technology. Use this integration as a benchmark to determine where they are on their trip.
12. Kim should have been the voyager equivalent of Bashir, not very liked at first, but evolves into a cool character (perhaps due to Paris'influences). This would be so much better then having him be the "honorary red shirt".
13. Tuvok had potential, but his biggest flaw was that he didn't contrast with the rest of the crew. Show his fighting prowess and his inner conflict. Make him a tad "logically paranoid" and have a touch of fear from the rest of the crew of having a powerful psychic on board. He should have shown his fighting prowess more and showed his extreme training with martial arts he mentioned from time to time. Also, he was the infiltrator of the Marquis. Make him hated and feared by those members of the crew, and give it enough of a justification to make the ship interesting.
14. Races should be cool. Other then the organ races (edit: Vidiian: I love these guys and they have serious potential), I can only remember a couple of the races that weren't used as a convenient plot device. Make the new races mean something and make fans seriously regret not having them in the alpha quadrant.
14. That federation officer that had become a serial killer, would have been so much cooler, if they would have been showing his rehabilitation, instead of poof, your rehabilitated.
Perhaps developing a "silence of the lambs" relationship with one of the female members of the crew.
15. and finally when they finally go back and return to their people, there should have been at least an inquiry and/or a court marshal into the actions in the delta quadrant.
And throw Janeway in the brig for her actions.
Even if she could rationalize her actions, it would make for a last bit of storytelling.
How trek doesn't always mean living happily ever after.
The things I liked about Voyager consist of the following:
1. The Doctor
2, Seven: originally I used to make the joke that it was seven's breasts, but honestly, she was a descent actor who managed to steal the thunder of the characters around her on acting alone.
3. Captain Proton.
4. Leonardo Davinci (played by John Rhys-Davis...if there was ever a character that should have pulled a Professor James Moriarty, it should have been him.)
...and have him get into bitter arguments with the doc :D
That is my two cents
since I originally wrote this, I've calmed down on Janeway considerably. Kate Mulgrew is a damn good actor with a character that stunk.
I would have made her more of a nerd and played off her rationalization to Chakotay's passion.
edit: The more I think about it. Chakotay would have been better if they have switched actors.
My choice would have been Lorne Cardinal
He can do silly and he can do scary, plus being Cree, he would have pushed back a bit from the new age garbage that voyager pushed as being native american.