1) Get rid of Paris or at least change him into somebody interesting
2) Make Torres hate her human part
3) Leave the doctor grumpy and make him less of a comic relief
4) Make the ship bigger (maybe 500 people), keep the Maquis ship in the shuttlebay like the Maru in Andromeda.
More people means there can be factions on the ship instead of one happy family; also, many people can die.
5) Have a group of Cardies on board and make the Maquis less likeable
6) Make Neelix cooler
7) Have a whole season where they need to stay in one area (maybe waiting for a wormhole to open)
8 ) Make supply problems an issue
9) Get Rid of Naomi Wildman
10) Less technobabble