The couple in TNG "The Survivors" was able to operate a replicator with the fusion reactor in their basement.
For a starship, limted access to the food replicator seems odd. And with the warp reactor mostly running at max, it's hard to believe there would be much of a power problem.
I mean, if a civilian like Quark could run several holosuites on DS9, which doesn't even have a Warp core...
They should have problems with space, some rare materials they run out of. But fuel and power should not be a problem. Not with everyone around them (including civilians) having spaceships.
There's also no reason they can't make more shuttles.
Imo, their problem should not be that they're weak, but that they are so strong (and are stuck in a faraway place), they can't help becoming players.
An actual series arc beyond "going home", including a series-long adversary, would have helped as well.
Let's be honest here, "On a long voyage" really is only good for 2 seasons or so. After that it just drags on if there's nothing else.
Now, if the plot of the series was the 8472 invading and wanting to destroy the Galaxy (nothing to do with the Borg, though they can get involved later) and VOY having to put together an alliance to stop them as well as find a way home, that would add to the show as well.
I really liked the idea someone suggested that it should have been an older class starship, perhaps on its last mission. All that bio-neural stuff didn't do much anyway. And would have made EMH a much grumpier figure ("just look at this primitive equipment I have to work with. I'm a doctor, not a miracle worker")
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