1) Caretaker part 1 should have been the season fanalie of Season 1. Killing off the XO, Doctor and Chief engieneer all at once would have been a big shock.
2) The caretaker had spent months bringing in ships from throughout the galaxy. We should have encountered more of them. The Seska storyline would have been more interesting if it were a Cardassian capital ship that was trying to make alliances and trade technology with the locals. Perhaps groups from similar parts of the galaxy might form fleets to go back home. Voyager could join such a fleet that might include: The Equinox, a Romulan Ship, Tholian ship, maquis ship.
2) Either Nelix, Kes and seven needed to wear Star Fleet uniforms, or the Maquis didn't.
3) Kes should have aged 10 years for each season. Havinf children and grandchildren along the way. I'll bet her biological clock going off would be alot more urgent than pon far!
4) More than one, indian, vulcan and bajoran.
5) The science officer should be higher ranked than an ensign!
6) Harry should have been the borg crew member instead of Barbie of Borg! He should have been an assimilated borg acting as ambassidor/spy for the collective. Being assimilated should be essential for his health due to the 8472 infection.
7) No borg queen! The queen destroys what make the borg unique and scary!
Chakotay's spirituality should not have been forgotten.
9) a post coming home season so we could see what happened to them.