In the earlier seasons I don't think it was as bad; they actually go back to a lot of things and address them. It's the later seasons that make me cringe due to the continuity.
Two things that always baffle me:
1. In "Dark Frontier" Chakotay tells Janeway that she fiddles with her combadge every time she's about to drop a bombshell. She never
does this at any other time, before or after this episode.
2. At the end of "Unimatrix Zero" we see Janeway in sickbay after being de-borgified, and she seems perfectly fine. It's all "oh just these damn spinal clamps" and nothing more.
Picard was haunted for years after his assimilation and yet Janeway's all fine and dandy?!
is what bothers me about Voyager's continuity; they address something once (mostly in the later seasons) and then never go back to it.
The fiddle with the combadge
was stupid and written by someone who obviously never watched the TV show or bothered to watch Mulgrew act. I would have had her start massaging the back of her neck
as her "tell" while she was walking through the debris in cargo bay 2, or had her sit down and just place her chin in her hand
while watching Torres & Seven play with the broken warp coil.
Picard lead the BORG in destroying Starfleet's armada at Wolf 359 (?). Janeway just punked the Queen. IMO she didn't have anything to feel guilty over.
My biggest complaint re: dropped ideas/"continuity" was that Axum was left on a BORG ship in a remote section Beta Quadrant. They made it sound "impossible" for him to return as a plot point, and yet he's on a BORG ship that can traverse vast distances in a blink of an eye.