Here are ten ideas that don't totally destroy the show as it was presented.
1. Make Janeway a true Ahab character, who's more in the background and whose decisions are very inscrutable to the crew.
2. Consequently, make Chakotay the shoulder that everyone leans on--- one thing that Beltran plays well.
3. Have a number of the crew abandon ship after "The 37s."
4. Introduce new crewmembers to replace those lost crewmen and busts like Neelix, Kes, and Torres.
5. Have Janeway found a new Federation in the Delta Quadrant... not to bring peace to the Kazons and Trabe, et al, but to surreptitiously extend Voyager's ability to search for ways home.
6. Make Harry Kim a human being.
7. Pit Tuvok and Chakotay against each other on a regular basis. Tuvok's mordant wit was underused on this show.
8. Make Tom Paris a true ne'er-do-well. His insubordination in season two should have been real, not feigned.
9. Have a story arc with Janeway's Devoran love interest. They had some chemistry and he should have been in at least 5 episodes.
10. Seska should have returned to Voyager as a vital member of the crew, AFTER betraying the ship. She was too good to kill off so easily, and the dumb production staff knew it.
And now a bonus suggestion...
11. Seven of Nine should have decided to return to the Collective late in the final season.