The Kes splinter story was in the String Theory trilogy, and it went a long way to redeeming Kes after the awful Fury. Kes is one of my very favorites, she and Janeway are my top two, so I really hated how her character was damaged so badly in this story.
I'm guessing JL didn't read the script before she agreed to do this story.
I think Fury is so bad it would've took a massive rewrite to make it work. A different, better story should've took it's place.
I totally agree with your statement.
When it comes to characters, Kes Chakotay and Janeway are my top 3 Voyager favorites.
As for "Fury", I know that there are those who question my theory that those in charge made the story just to show the finger at the Kes fans who wanted her back. But honestly, after all those years I still can't find another reason for them to come up with such an awful, meaningless story. It had no purpose at all and didn't fit in or affect the ongoing Voyager saga as such.
I don't understand why JL agreed to participate in this destruction of her character but she did at least do one good thing. What I've read or heard, the original plan was to kill off the character but JL made them change their minds about that.
And yes, "Fury" was so bad that it is impossible to make it better. There should have been a totally different Kes come-back story, most likely my "Coming Home" story which can be found at the Kes Website!