Actually, the conflict between the Maquis and Starfleet had popped up a few more times during Season One.
How was Janeway's handling of the Vidiians a problem?
Regarding Janeway handling the Vidiians...
If the situation in
"PHAGE" is what is being referred to, I completely agree that she handled that badly. VERY badly.
Neelix's lungs were
stolen by those two. She is finally able to capture them... and her solution is to
let them go?!
That sends a very,
very bad message to her crew. She's basically telegraphing to them that their safety doesn't mean anything to her as long as her principles are being upheld. She's saying to the crew, "I'm not going to bother defending you or fight back when you have been violated." Why would anyone want to follow a leader who doesn't have their back when they are attacked?
Especially the Maquis crewmen.
Janeway is
supremely lucky that the one Vidiian decided to help Neelix. Otherwise, there could (and frankly SHOULD) have been a mutiny.
(And before you throw in the 'only Janeway gets picked on specifically out of all the other captains' card, Archer did the same thing in season 1's "FUSION". And I absolutely
hated his decision there of just letting Tolaris go after he basically mind-raped T'Pol. At the very least, he should have been kept under guard until the Vulcan High Command can come by and grab him. Not just get a stern talking to and get released to the Vulcan ship.)
I don't think this is what TPTB initially wanted for the show. The entire setting for the show kind of lends itself to an almost mandatory arc of some kind which the first 3 seasons had loosely. Then the ratings started dropping and UPN mandated TNG-Lite.
I agree that the entire premise of VOY almost
expects serialization, possibly even more so than DS9... especially since with VOY, there is no chance of getting new Starfleet crew for transfers, replacements for deaths, etc. And the first 2 seasons did have some semi-serialization and some arcs. I wouldn't say it disappeared completely from season 3 onward, but it was certainly cut back.