A two parter or story arc centering on a full scale mutiny, with them fighting for control of the ship, deck by deck. This is in general something I regret never happening on any Star Trek series, but it would have been especially appropriate for Voyager given the setting. I think real life mutinies are generally the enlisted men rising up against the officers, so there would have been no need to involve any of he main cast, although featuring recurring characters that the audience already knew amongst the mutineers would have been a good move. It could have been a Maquis lead thing, but some disgruntled Starfleet personnel could participate as well.
More episodes in general early on focusing on Starfleet/Maquis conflict, aside from the couple they did. Specifically a Tom/Chakotay conflict episode early on.
Episodes focusing on Kes's rapid aging (she didn't really age on the show even though we saw a significant chunk of her lifespan). This would be easier to do if you kept her on the show for the whole run.
More Hirogen episodes. The most interesting alien they created for the show.
A comedy episode with Janeway trying to figure out ways to spur romantic relationships amongst the crew. If you think about it, for the ship to be able to function as a "generational" ship for 70 years or whatever, people needed to be having way more babies than they appeared to be having, so it makes sense that that's something she would be worried about. They sort of did one like this if I remember, but Janeway had a very hands off attitude towards it when it would make sense for her to be concerned about what would happen down the line if the first wave of crewmembers didn't have a "replacement level" amount of offspring.
Give Tal Celes her own episode. She was only in an episode + a cameo and was still more interesting than like half the main cast. Ideas include going into a rough backstory on Bajor (maybe explaining her anxiety), giving her an ill-fated romantic relationship, with her hypochondriac friend getting jealous (she seems ripe for heartbreak) or putting her in an awkward situation by herself where she has to save the entire ship. You could combine all three of these.
Leave the Borg out of the finale and have it be a callback to Caretaker.