Reduce it to 4 or 5 seasons. 7 just seemed to drag out the inevitable "we're gonna try to get home but it won't be 'this' episode".
Reduce the cast to about 5 or 6 regulars. Having 9 requires the writers to create stories just to put the characters in to give the actors something to do (like Neelix after 'Fair Trade'). Either that or have the atrition rate of regulars very high.
All the major points have been addressed, like continuity, abundance of resources, etc.
I would like to have made the Kazon more badass, and not just a Klingon clone. Also, maybe have Janeway piss off a Kazon commander in the pilot, and he vows to hunt Voyager down, thus giving Voyager an ongoing enemy, similar to the Cylons chasing Galactica.
Character-wise I would've made Janeway younger, perhaps even the first officer of Voyager and the Caretaker kills the captain instead. That way Janeway would be thrust into the role and we'd see an up-and-coming captain instead of the experienced captains we always see (although Sisko started as a Commander, didn't he?). She would also have to deal with Chakotay a lot more, as he would have a lot more experience of commanding a ship.
I would ditch Tuvok, Kim & Kes, and make Neelix more of a Galen-type character (from Crusade).
Voyager would be more of a warship, like the Defiant, perhaps a failed Defiant-prototype. She would have a squadron of fighters assigned to her, which would make them very handy to have in the Delta Quadrant.
Season one would end with Chakotay conducting a mutiny, forcing Janeway into the airlock, ready to blow her into space.
Season two would end with Voyager forced to land on a planet and the crew forced to make a colony for themselves as they can't get back up.
Season three would end in Borg space, with Voyager under a Borg tractor beam and Janeway apparently assimilated.