- The first season would deal with the two crews having to learn to co-exist, with things extrmely tense because Janeway is so inexperienced as a command officer Chakotay comes off as more assertive and showing more command qualities than her. But Janeway would earn her keep and respect by using her scientific knowlege and analytical mind to help their survival, like rigging a way for them to use the Nebula matter as fuel by making a fuel converter with B'Ellana, or harvesting water from comets, etc. She'd also begin using her scientific analytical skills more for tactical uses as well as survivalist science. They'd also have to deal with Cullah's attacks, as Voyager is the most advanced ship without a major power as a backer his group have encountered and they want it not just for the tech but for another reason, "why" is not revealed until season two.
- Tuvok would be a Vulcan who isn't as adept at sciences and such (explaining why Janeway was Science Officer), although he retains a logical mind and is more distrustful of the Maquis, and although he comes to accept them as shipmates, he doesn't form any true friendships with common Maquis and has a purely professional, although respectful, relationship with Chakotay and Torres. He'd be more of a First Officer to Janeway, while Chakotay is on the bridge as the Maquis rep.
- Neelix is an older guy than what he was, a soldier who went AWOL in the Talax-Haakonian war and used his skills to survive as a merchant, although he found himself trapped as a scrap dealer on the edge of the periphery until Voyager came along. Now he sees this not only as a chance to make up for his past cowardice but also to get out of the Periphery and closer to the Major Regions without attracting the Kazon.
- All the alien races use different kinds of FTL drives, different weapons (no Phaser, lasers, disruptors, cannons, torpedos, etc), different shield-type things (differently named, at least), and have most of it turn out to be just as good if not comepletely superior to anything any pre-existing ST race has (aside from the Borg).
- On the worlds they do find with markets and stuff, they all use a Capitalist economy with currency, so Voyager has to trade for money, and some of the crew even take jobs for money, and the Ship itself could do work as a courier due to their neutrality, or investigate missing vessels (a way of meeting the Vidiians) for money.
My reasoning for why VOY can't tell where they are is that most of the stars in that region of space were blocked from Federation view by intervening nebulae, gases and other stars, so they wouldn't have ready fixes in star-mapping. That happens in real life, you know. We simply don't know what the other side of our galaxy looks like. We don't know what the stellar regions look like behind nebulae like the Horsehead and Orion Nebulae.
the ending of S1 of VOY would have VOY fighting one of the massive Kazon Carrier ships which is going for an all-out attack to keep VOY from leaving the Periphery and making it to The Major Regions. The Carriers usually don't fight even though they're the best armed Kazon vessels because they have families and children and non-combatants living on them (as Cullah's group have no homeworld) but they thought there was no other choice but to use it's heavy weaponry.
Voyager has it badly damaged, and Janeway is faced with the choice of destroying it even though she knows there's more non-combatant Kazon on it than combatants, or just running away. Tuvok tells her that if they don't destroy it, it'll transmit their coordinates and likely they'll face all the Kazon in the area in a swarm attack before they leave the Periphery, and they can't survive with the damage they've taken. So Janeway has no choice but to destroy the ship. And despite Chakotay telling her that she's gained more respect from the Maquis and proven to be at least a capable captain to her detractors in the Fleet crew, Janeway leaves for her quarters to retire for the night.
The last scene would of her making a log entry of how "today I got lucky, I destroyed an enemy vessel with thousands of Kazon aboard...I probably killed a lot of Kazon who weren't fighters...families, mothers with their babies, children...and I've been congratulated for it. Maybe I'll get luckier, next time I could destroy more ships and kill more innocent people..." with her being unable to finish the entry and then the credits would appear on screen.
The opener of S2 would have Voyager making it out of the Periphery, past Cullah's group of Kazon Pirates and enter the central core where the major powers and central worlds/commerce areas and stuff are, hoping they can find some ports to stop and do repairs and maybe find more information on where they are.
The dominant power there is The League of Spacefaring Civilizations, a multi-species group that was originally formed as a military alliance for mutual defense against their greatest foe (the 8472 aliens, who in this version are naturally from our galaxy and are classified as the "Fluidics") that eventually evolved into a Federation-esque group, only with more of a military bent. They put less emphasis (little to none) on purely scientific or exploratory endeavors and dedicated their sciences and star forces to military applications. The only explorations or archeological missions they undertake are to uncover and seek out alien technologies for their own advantages.
They became so military-oriented that they eventually started ignoring the lesser wars and plights of non-League civilizations (not doing anything to help the Vidiians fight the Phage, or end the Haakonian Occupation of Talax) so they could focus more on their own defenses (because they're so scared of the Fluidics who are IMMENSELY powerful). They're not bad guys or some generic space military state, but they have military bases and garrisons on practically every League world and colony; however the civilians all undertsand their need and are grateful for their presence.
Imagine the meeting from the beginning of Trek VI, only they're discussing increasing militarization and mothballing their scientific and exploration branches to increase military spending (they use a capitalist economic system).
So as long as VOY obeys their laws and stuff, they can use their ports and trade, and the League may even rescue them from Kazon Pirates if it's in their patrol space, but once VOY leaves League influence (or even the outer reaches of League space, at the very beginning of entrance into the nebulas/asteroid fields/empty systems leading to the Periphery), they're on their own against pirates and stuff because the League isn't interested in defeating the Kazon pirates once and for all and saving anyone in the periphery.
Size wise, they're a little smaller than the Federation, and maybe technologically on par in some areas, below in some others (because of the military bent) and superior to them in ship design and military technologies.
The League's best ship would be similar to the Voth City-Ship, which is a "Mobile Command" they only have a handful of. They serve as mobile HQs and Super-Flagships. To borrow from Star Wars they have automated battle drones that serve as their smallest craft (sorta their take on Fighters). Like the Battle Drones from TNG's "Arsenal of Freedom".
As for the League's weapons, they're basically supposed to be what if the Federation was near-totally militant with little to no scientific or exploration divisions. This would mean they're more rigid in tech development and don't have the "Jack of all Trades" style that the Federation uses. But they don't grow expendable clone armies to be sent out to die or make mass-production warships that're meant for ramming and stuff like the Dominion does either. They try to make mass-production ships that can hold up in a fight, and their military is made up of trained League citizens who volunteer for service (like a regular military).
So their ship-building skills are below the Dominion's because they try for quality AND quantity, and they're more rigid in design than the Federation. But they do have superior vessel design with more powerful weapons, hulls that are harder to breach, good military training and tactics, more maneuverable (isn't very good as a warship if it's a lumbering brick).
To command a Mobile Command, you have to be at least a Senior full Admiral, or a Fleet Admiral.
In general, their ships are larger than Federation or Dominion ships, with the Sovereign maybe being their equivalent of a Heavy-Destroyer, but not a Cruiser.
I'd keep Lon Suder alive, although I don't know if I'd eventually kill off Seska or have her escape to try and join the League Military after ditching the Kazon (who she'd join ultimately).
The other powers would be the Krenim, who're going through a new expansionist campaign due to a military uprising on the Krenim homeworld against the Ruling Imperial family.
The Devore Imperium, who're very anti-telepathic, due to the "Great War" 2000 years ago which involved telepathics enemies who used their abilities to great offensive effect.
The Heirarchy and the Malon, just to add some more names and stuff in to flesh out the region.
And the Lokkirrim and Think Tank, to set up the "AI War" story for later on in the show.
That's it for now, but I'll post more later.
