I've been trying to decide what I would do, and honestly I haven't a clue.
Part of me thinks that the entire Borg plotline should have been wrapped up in the second part of "Unimatrix Zero." (And by "wrapped up" I mean either the Borg would be schismed into separate relatively non-threatening sub-collectives, or the Zero "defect" would be augmented to liberate the entire collective.) I don't think it's disbelievable if it's essentially a Borg civil war that does them in.
Voyager's just helping.
I'd like to have seen the Vaadwaur or even 8472 return as final villains, but this would be primarily as a device to get the crew home. I'd have also like to have seen the female Caretaker potentially make a return, possibly with Kes having to help save them.
I would have definitely eliminated the regular contact with Earth, but the crew would have actually gotten home in the fourth and third to last episodes. I'm not exactly sure how I'd do these two, but it would be one final epic. I had an interesting idea that in these episodes, whatever happens, halfway through
Voyager would have finally taken irreperable damage to her warp drive, and would be forced to land on the nearest habitable planet. At first, the entire senior staff is determined to fix the ship, but they eventually realize that this is impossible and try to build a life here. This is where the contact with the Alpha Quadrant would come in again - the crew would be able to send one final message telling Starfleet where they were. The ship would eventually be dismantled to build a settlement.
Flash forward about five years. A
Galaxy-class starship arrives in orbit to bring the crew home, who only go reluctantly. These final two episdoes would be called "Homecoming" and being about dealing with all the consequences and adjustments they have to make upon returning home. A recurring theme would be that, even though they are finally home, most of them really feel quite as much at home as they did on the ship, and eventually the crew would be given a ship to go back to their colony.