I've already done my own version of Voyager, with the ship being an Ambassador Heavy Cruiser (and the plot being more like Andromeda where they go around building a Delta Federation, the 8472 being the main villains of the entire series).
But I've gotten a new idea for another new take, and I'd start off by having the Caretaker be a much bigger influence on the area they're in:
He'd be this Mad God who experiments on various folks from around the Galaxy he's imprisoned on Ocampa, and he's kept all the sentient species for around 20,000 LY all at a subjugated level to prevent any major spacefaring empires/federations from forming and doing anything to interfere with his rule. His mate left him long ago, tired of this madness. The Kazon are his servant species, basically "God's Children" who help enforce his will when he needs them though he experiments/tortures them as well.
His latest pull is the transport ship Janeway and Tuvok were on, Tuvok bringing in some Maquis terrorists while Janeway had a schedule mixup and needed the transport to get to her new assignment.
Either they bring some Alpha Quadrant bacteria with them that has a nasty result on the Caretaker and kills him, or his latest madness was the last stage of a terminal disease that kills him. He activates a self-destruct and Janeway and co lead a jailbreak on the Ocampan world where they evacuate everyone (and there are folks from all over the DQ there, not just the Ocampa) onto the ancient vessel that the Caretaker used to come to our Galaxy in the first place.
The Kazon break up into groups, with one group deciding that they will avenge their dead Master and take his "Legacy" (the Nacene ship) from the "Invaders". Neelix is a Kazon who had long ago tried to rebel against his God and was imprisoned as a "Heretic" and helps Janeway and co escape.
The Nacene ship is massive, capable of sustaining thousands of people (though the crew is much smaller, and so they don't need to resupply and crewmembers can disappear into the ship's expanses for entire episodes) and has incredible technology and weaponry but not compatible with the DNA of any of the crew to take complete control so the ship's AI takes over functions. It scans Janeway's form and assumes a human Hologram form (Robert Picardo) as a "form you are comfortable with". He'll help them with basic ship functions like navigation and low-to-mid-level weaponry and disembarking/re-embarking on planetside missions but not with much else unless he concludes its for good reason.
They do have other vessels stored in the ship like the Fed Barge and other vessels from the other captives, but most of them are okay with staying on the Nacene ship with its superior power.
Immediately afterwards, the surrounding regions all begin to react to the death of their Mad God and we see what kind of social/cultural/political reactions there are when "God Dies", like the creation of new Empires and wars or cooperation.
Plus, the Caretaker also swiped groups of Klingons/Romulans/Cardassians/Ferengi from the Alpha Quadrant and they also all escaped on their own ships when the Array blew, so they can show up as recurring characters also on the move.
How's that?
I like it.
