It's a reasonably popular fan theory. That she was a great science officer, but one who just got promoted too quickly, and possibly outside of her comfort zone. By Admiral Paris maybe? She seems to have been his "teacher's pet".
So this thinking goes: if we accept this idea that USS Voyager was Janeway's first command, and that the Maquis mission as her first major assignment as a Captain, then we can justify her helter skelter characterization over the course of the series as being her kind of learning command responsibility as she goes along... which accounts for the occasions when she gets it wrong, or allows her "book learning" (eg. a quasi-religious attachment to rules and regulations over common sense) to over-rule the more immediate alternative options that might be available to her.
At other times, she slips, and gets a little... unhinged? Unsure? Loses her confidence. Whatever we want to call it. I don't think it helps that she doesn't have the safety net that other first-time Captain's have, of being able to get advice from Starfleet Command. She's all alone out there in the wasteland.
Whichever way, I don't see it as a bad thing. I think it enrichens the character, makes her more vulnerable, relatable and "real".