At the time? I have no idea what I would have done.
From the point of view of hindsight, if I where to go back and "fix" things?
I would kill Chakotay, and re-shuffle the deck basically.
Tuvok would be promoted to First Officer. Paris would eventually be promoted to Lt. Commander and Kim to junior Lieutenant, but neither right away. Maybe Kim half-way through the season and Paris at the end. Neelix would be made a Crewmen and begin wearing Starfleet gold uniform, and start bouncing around departments. He wants to be in Security, but he's always been a jack of all trades so he keeps jobbing around all season 4 trying to find his knack.
Eventually, he ends up replacing Kim at Ops, as Kim becomes Chief of Security and Tuvok finally takes Chakotay's chair, which would be left empty as a symbolism thing most of the season.
Chakotay's loss would hit Janeway especially hard and for most of the season, she'd be much harder and cold even. She resents 7 of 9, this ex-Borg, for the crimes of the Borg, but her humanity can't allow her to just drop her off at the next planet. It's a human woman; a girl when she was assimilated. She was 'abused' by the Borg the same was Chakotay was 'murdered' by them. Kes and the Doctor would be the two to really deal with Seven that first season, Janeway getting into the mix more as it goes on.
I'd have the ship itself take significant damage in constant hit-and-run attacks from a disorganized Borg Collective (as a result of the on-going 8472 war; I'd also give 8472 a better name, their own name for themselves, eventually.) I'd also have them slowly phase out the shoulder color uniforms and upgrade to the gray-shoulder DS9/FC ones as the old ones where replicated away/back to be cleaned. Sort of like how "Generations" had both sets, I'd use season 4 to do likewise. By season 5 they'd all be in gray-shoulders.
I'd keep 7 of 9 looking more Borg longer. At least 6 episodes of consistently reduced Borg make-up. The last thing to go would be the eye-piece and basically, she'd be pretty ugly until she finally lost that and got hair. Because I don't like how they just snapped their fingers and humanized her so quickly.
I'd have Kes gradually become an advisor to Janeway, becoming her reverse Guinan of sorts. Old and wise, young and naive, both make their points by looking at it from a unique way. I'd juxtapose this with her aging; I'd add streaks of gray to her hair, here and there, more and more. Some light age make-up. Eventually though I'd find some miracle 'cure' for her aging.
I'd end season 4 with the same basic episode, "Hope and Fear" only altered to account for the differences. Arturus still wants revenge for Janeway's interference that destroyed his world, but in this version, Janeway in the brig with Seven on the Dauntless is... defeated, almost. Morally, anywho. Seven manages to rally her, though, which is a big step for both of them. It connects Seven to her humanity by making her realize she wants to be herself and not Borg again for the first time, while also making Janeway snap out of her depression over Chakotay's death.
I'd have their contact with the AQ, and the word of the slaughter of the Maquis, be much more of a story arc. B'Elanna lost Chakotay and now this? She's also the de facto leader of the Maquis part of Voyager's crew. So on the surface she'd buck up and brave the storm, but underneath she'd be becoming suicidal over the course of the end of that season and into season 5. Tom is able to snap her out of it though, and their whole relationship arc goes much quicker. They'd be married by mid-season 5.
Season 5 otherwise would be mostly the same, though I wouldn't do the Janeway's regrets story line from the season premiere. I'd have her be with the rest of the crew, bored witless at the void.
I'd do a variation on the "Dark Frontier" story-line, where Janeway wants the transwarp coil - but in the moment, she loses her focus on that and just wants to hurt the Borg, and Tuvok had to pull her back. They get the coil and make a monumental leap forward towards home, a good 25,000 light years. It renews everyone's spirits, but Tuvok's rebuking of Janeway puts a strain on their friendship for a little bit.
The Equinox arc would be extended, 2 or 3 episodes at the end of the season 5 and then 2 or 3 in season 6. I'd shake it up by having the Equinox be the opposite of Voyager; Equinox had also been chasing 2 or 3 Maquis ships when pulled in, and they lost their senior officers when their bridge was destroyed. So the crew pulled together on the Starfleet ship, but didn't become a Starfleet crew; they became a Maquis crew. Which is how they got so much farther so much faster. Voyager's sustained damage from the 8472-Borg war hit-and-runs would be juxtaposed by Equinox being lavish and having her bulkheads intact. It would present Janeway with a real nagging doubt about if she had done right by following SF principles when the Equinox has faired so much better.
I'd also have the Maquis captain be a personal friend of Chakotay's and B'Elanna's. He would even try to feel B'Elanna out concerning a mutiny and taking Voyager's resources. Of course, the revelations about their 'crimes against humanity' would convince Janeway she had been right all along and B'Elanna that this former friend was an enemy. But B'Elanna would be tempted by the promise of 'family' in other Maquis. Equinox would be guilty of more than just killing the one species of alien; they'd have taken mercenary jobs, used SF technology to shift the political balance of power for species who could help them.
The arc though would give Voyager time to be repaired and start to look better, ship-shape again, before they realize the help they're receiving are the spoils of unjust wars. In the end, Equinox would be destroyed with most of her people, but a handful - a dozen or so - would survive. They would at first end up in the brig, but it's a temporary solution. They can't afford a dozen prisoners draining resources and contributing nothing, so Janeway does what she did originally and strips them of rank and puts them to work as lowly Crewmen.
I'd come back to their story though, perhaps have the lot of them want to leave the ship and settle on a nice DQ planet, but Janeway has reservations - both of letting them leave and if others might follow, and because of their past crimes.
I'd establish regular SF Contact in season 6, like was done, but earlier. I'd do "Pathfinder" like it was done, but instead of being a one-time thing, it's monthly from the start. I'd show more of the crew's families. I'd have Seven find out about grandparents, aunt's and uncles, cousins. Make a real connection to home. We'd see Naomi Wildman's father. Hell, we'd see Samantha Wildman again lol. We would see Tom and Admiral Paris start to talk, to heal. B'Elanna and her mom. Harry and his parents - and Libby. I'd also have B'Elanna pregnant in season 6, and so Miral would be around as an infant all of season 7.
Season 7 would all be about getting home and resolving old issues. An end to the Borg/8472 war by having the Borg Queen ask Janeway to negotiate a truce. It's a trick of course, but Janeway despite her hatred for the Borg, can't refuse - because the DQ has been torn apart by the war and as much as she wants the Borg destroyed and fears 8472, the collateral damage is to much for her to ignore.
At some point the Borg Queen would pull a double-cross, but she'd end up paying for it. Voyager would escape as the war re-ignites and the cease fire halted and make use of the transwarp network to make it into the Beta Quadrant; they're less than 30,000 light years out, seeing the occasional familiar species like a Klingon trader or Vulcan merchant out on the fringes. It's still a journey to go, but it's a big step closer to home. And allows regular communications with Starfleet on a whenever basis, even if it's all time-delayed save for the monthly wormhole/pulsar window.
The Doctor would have a similar rights trial, but the resolution would be far more apt and he'd be granted sentience like Data was.
The series finale would be a 4 or 5 episode arc, where they learn that 8472 has all but destroyed the entire Borg Collective. The Queen would be back once more, and we would learn the origins of the Borg. 8472 have destroyed the Borg home world, and discovered a secret not even the Queen herself knew that explains the Collective's odd but obsessive behavior with humanity: it was humanity that created the Borg. Sort of.
Taking a page from the Shatnerverse novels, we would learn that the V'GER probe had fallen into a black hole and traveled through space and time to over 1,000 years ago. This race of sentient machines had repaired V'GER and sent it on it's way, but they had also learned of organic species from it. They where curious and sought out these carbon-based life forms, but didn't realize how fragile or emotional they where. They pursued 'experiments' in a logical machine-like thinking fashion, which was in truth horrific of course, and began to integrate organic components into themselves. Eventually a great civil war erupted between two factions; purists and those curious about organics, and what survived was a cybernetic life form with quite a bit of memory/program loss. It become the core of the collective, with broken protocols.
"Assimilate all knowledge about Advanced Organic life forms worthy of further study" became "Assimilated all Knowledge, Advanced Organic life forms, worthy." while "Add distinctive biological and technological samples for your own further study" became "Add biological and technological distinctiveness" so on and so forth.
This core of the collective also retained incomplete data from V'GER about the creator, where they came from, but nothing conclusive. Nothing that made them able to say "ah-ha! Humans!" - but there was enough of a similarity once the Borg encountered humanity to make them obsessed with such. At the same time, the reason they only ever sent one ship instead of a whole fleet - the reason they 'held back' from forcefully assimilating Earth and humanity - was a desire to complete V'GER's mission. It's mission. It wanted humanity to want it.
8472 has discovered this. Discovered that humanity played a role in the creation of the Borg without ever knowing or intending to, and they want revenge for all their losses. The Borg have been all be destroyed; now 8472 wants humanity wiped out.
To which, the Borg Queen, desperate to save the last shreds of the collective, proposes: we work together, or we all die.
The Queen and about two-dozen cubes and spheres, open a transwarp conduit and take Voyager home to Earth. Which causes quite the reaction. It's not quite a happy homecoming, what with 20-odd Borg vessels and an impending invasion by a species no one in SF save Voyager has ever done more than read about. We would juxtapose reunions and promotions and transfers with the pending 8472 invasion.
If possible, I'd bring in some people from past Treks for guest spots at the end. Kira and the Defiant, Riker and maybe I'd have him already be on the Titan, stuff like that.
Some at SF blast Janeway for bringing the borg to their doorstep, some push to wipe out these last Borg ships and deal with 8472 alone, but Admiral Paris puts an end to it all, pointing out: alone, we stand no chance. What choice did Janeway have?
They devise a plan and the Queen provides Starfleet with almost the whole of the Borg's knowledge. It's too much to deal with then, but they realize the Borg's defeat rested on their inability to think 'outside the cube' so to speak. That SF ships augmented with Borg tech and controlled by individuals could stand a chance.
We'd have an epic huge fleet battle, like we had in DS9 in the actual 2-part finale. In the end, it would be diplomacy that stops the conflict. Janeway and company are able to convince 8472 that the Federation didn't make the Borg; that an ancient primitive probe simply inspired their founders. That the Borg pose no threat now, nor does Starfleet and as proof, Janeway has the entire Alpha Quadrant Armada (SF, Borg, some smatterings of Klingon and Romulan ships) stand down weapons and shields. She basically hands 8472 the knife and puts it to her own throat, so to speak. This, finally, convinces them.
The Queen doesn't like this and tries to launch a final desperate attack, to which 8472 swat her and the remaining Borg like flies, finishing the collective once and for all.
The final scene would be of Admiral Janeway and crew being honored in front of a massive crowd, Voyager landed on the grounds of the presido behind them.
So yeah... that's how I'd re-do it.