1) No chakotay- make Tom Paris an older rogueish man and a commander.
2) Crew finds out Seska is cardassian but she stays on anyway...no stupid pregnancy. I always liked Seskas acidic wit...instead of a cardboard cutout villain she would have worked better as a foil
3) B'lanna looks and acts more klingon
4) No neelix
5) No holodecks
6) Scarcity...if you everything you need where are the plot twists?
7) The maqui and the federation do not have to be enemies but they do have to do things differently.