Pretty good analysis Tyyr, and I agree with most of what you said:
1) Maquis.
I would also give them the choice of whether they want to stay or leave the ship, and let them go, with little to no supplies, as Voyager cannot spare any, being rare...
2) The Ship.
I would show the battle damage, worsening more and more, with alien hull plating replacing the original, damaged plates.
Alien com panels replacing original starfleet panels, etc...
Torpedoes would be used sparingly, as they would not be able to replenish them since they need all avaialble material, AM included, on more vital ship parts (like engines, and shields, and Phasers).
Would stop looking pristine early on with all the battles its going through...
3) Supplies.
I would see every type of supplies being needed.
Raw materials for the hull alloys, plasma conduits, basically every ship's parts, plus the AM.
Hydroponics bay is good, as well as a good chop shop, because not all parts can be replicated, some may take more energy, and may be easier done the old fashion way.
Many negociations, many through force for the rare, important supplies.
Technology exchange if neede...
4) Janeway.
Have her play straight after some nightmares about her rule-bending sessions.
Then have the crew do everything they can (especially the Maquis, with Chacotay leading) to obtain supplies, sometimes through questionable means (or "anyway we can" in Maquis speech), and have her find out in season 4, and see how she reacts, if she'll punish the guilty, and if so, at what cost to the crew morale, a crew who got used to getting things done, not worrying about getting what they need to survive, etc...
5) Equinox.
Keep the two ships, and have the weight of added lives depending on her be felt by Janeway.
Have her harden up, decide she's had it, and fuck the rules.
Transform the show into what good intentioned people can become when desperation hits, and make Voyager grittier.
6) Relationships.
Pretty much as Tyyr said: have them pair up, makes for more interesting stories when one looses a loved one due to "stupid" command decisions...
7) B'Elana/Tom.
Have them pair up early (end of season 2), like Tyyr siad, then kill Be'lanna in season 4.
Make Be'lanna less a whiny bitch and more an angry half-Klingon Chief-Engineer ("You want to do what to MY SHIP?").
And still kill her off...
8) 7 of 9.
Data with human potential and in a hotter form.
Keep her, allow some evolution, make her part of the crew, and when people are Fed up with how inefficient Janeway is, make Chacotay the Captain and her as First Officer...
Oh yeah, keep the catsuits though...
11) The Borg.
DO. NOT. PUSSIFY. THE. BORG. EVER.
Avoid at all costs and have different events bring 7 of 9 to the ship (Voyager's version of Hugh, for example, but a Hugh they keep because it wants to stay).
The Borg remain the big scary Badasses they were, and NO BORG QUEEN DAMN IT!!!!
12) Neelix.
Kill him off.
He's a moron, admitted many times at not knowing much of what he talked about, and after season 2, when Voyager was out of the territories he had covered, was franckly useless.
Have him say (again) how he knows about the alien of the week, and make it turn out real bad, get captured with a few crewmembers, and killed while Voyager attempts to save its crewmembers.
Thay have to choose who they save, and Neelix isn't one of them...
Tyyr wrote:13) Return. I wouldn't end the show with Voyager heading for Earth. Voyager would arrive home with 2 or 3 episodes to spare. Save some time to deal with the multitude of issues that come up from Voyager being gone. Janeway's fate, the Maquis, 7 of 9, Tom, etc. How do people who might have moved on with their lives deal with finding loved ones who've moved on with theirs?
Great idea, but I would even go as far as using 10 episodes to deal with everything.
Oh, and one more thing:
NO GODDAMN BATMAN ARMOR OR TRANSPHASIC TORPEDOES...