Drop all the Maquis crap. The forced conflict would have been even worse than quickly forgetting to make pointless references to it.
Drop all the conservation crap, until the ship is about to be destroyed.
Keep part of the crew in the stasis chambers in the life pods, or the transporter memory banks. The idea is to shorten the bite out of the life span.
Jennifer Lien had a lovely voice but Kes was a disaster. Nobody can figure why she wanted to spend her entire life on a starship going away from her home. The regular crew came to Delta Quadrant in less than seven minutes so they would naturally at some level think they could get home faster than seventy years. Kes did not have that experience to give her hope.
Leave Chakotay his little spiritual hallucinator gadget. I suppose UPN told them to drop that part of the character. But after they had to get out of the Maquis dead end and after Seska castrated him, losing the religion pretty much finished off the Chakotay character.
Drop the Seska arc. Leaving the Cardassian spy on board wasn't terribly interesting either but her machinations had no motivation other than innate evil. They certainly had nothing to do with getting home faster.
Drop Tom Paris. What kind of a name is Paris anyhow? Sounds like a pseudonym for Gary Stu.
Roxann Dawson was at least lively. But drop the half Klingon stuff and just make her bad tempered and in over her head because of staff shortages. Modern Klingons are completely stupid anyhow. But the idea that this little woman would aspire to master the idiotic frat house hijinks of the Klingons is unbelievable. (And Moore couldn't figure anything to do with Torres because he can't think straight about Klingons.)
The idea that Janeway was schizophrenic is really crazy since the character with two personalities was Seven of Nine. There should be a happy medium between barking like a dog and helpless femme. Play up the sibling rivalry with Kim.
Always remember that EMH is a comic character.