I watch Star Trek to get entertained, primarily.
As such, stuff like plausibility or the correct use of scientific terminology in "science" extrapolated to the future, or even universe continuity take a backseat (though I like it when they get that stuff right, too).
And I must say that even though Threshold really is hilariously bad, at the very least it entertains me. More so, in fact, than many mediocre and unimaginative episodes (with a nasty alien of the week) that aren't even close to being as "bad" as Threshold. Those episodes are just ... bland.
So, to me it serves its purpose. Even though it has some of the worst science, and I would rather consider ït to have "never happened" from a continuity point of view.
(BTW I don't consider the episode to be detrimental to the characters of either Paris or Janeway, as they only started behaving strangely after some really outlandish stuff had happened to them).
I sympathize with your post.
I did say earlier that I wasn't sure if I had witnessed something brilliant or brilliantly bad when I finished the episode, but one thing I did not mention was that: Even though I wasn't immediately sure of what I had just seen, I knew it had shaken me to my core.
Whether it's for good reasons or bad, it definitely made an impact.
Talk about "out of the box". You would think this would've had eternal repercussions on the show and characters. It would've been ballsier if they had followed the current of the episode. The impact of the human race creating a new race of humans and leaving the offspring on the planet. What this bonding meant for Janeway and Paris. It could've changed the show forever.