Well, if we have to nit-pick, then all of the characters should have been dumped after season 3 because none of them had any arc to talk about.Why only Kes?
The Doc., B'Elanna & Tom's arc's continued thought out the series.
As for Kes.
Considering it was "popularity" that made Kim stay, maybe it she was the second character at the time on the low end of the popularity scale?
Maybe cause between her and Harry, they had the jobs that were easy to replace? Seven had Engineering skills and the EMH didn't really need a nurse.
She was starting to be treated more as a background character than a main one?
Me personally, I do agree with TPTB when they say they wrote the character into a corner. They gave her job that ended up limiting her participation and screen time. It didn't help that Picardo got the best lines which then allowed him to hog up much more screen time and dialog from her.
The fact that they made her afraid of her powers, instead of finding a better way for to use them limited her again.
I think her going from being over curious to being to wise too soon limited stories of her growing up.
The Kes we saw in "Twisted" IMO should have been how Kes was during the first few seasons. The wiser Kes was saw in s3, should have been s6 Kes, by that time she's learned and seen more. S3 should have been teen Kes, a little more rebellious and bit more of a risk taker.
However keep in mind, this is all in retrospect.
It's easy to fix mistakes looking back on them, much harder to see mistakes as there actually taking place in the moment.
I think in general, it's why it's so easy to criticize Voyager as a fan because we're all looking back on comment on how we'd fix it after the fact. I doubt that had any of us been writers on the show during production, that we would have caught the missteps as they happen.
I'm not so sure about any arc of Tom and B'Elanna. Sometimes I get the impression that their relationship came up just to show that they still were on the show. B'Elanna became superfluous when Seven took over her role as the one who could fix anything malfunctioning on the ship and Tom was also shoved in the background when Seven arrived. Both Tom and B'Elanna were better and more interesting characters in seasons 1, 2 and 3.
The Doctor did have an arc. But he became much too human with that emitter. He was more realistic as only a hologram. If they wanted an almost human character, they could have made him an android, like Data.
As for Kes, I totally disagree with the decision to dump her and I find the excuses for dumping her very shallow, to say the least. They should have been honest and said: "We wanted to bring in a sexy babe and had to dump one main character. We were going to dump Kim but when that magazine showed him among the 50 most handsome in their silly inside beauty contest, we kicked out Kes instead". That would have been more honest than coming up with those fairy tales about "not being able to come up with good stories for her". OK, I would still have been angry about their decision but at least they would have been honest.
I do agree about your statement that the Kes we saw in "Twisted" should have been Kes in season 3 and the Kes we saw in season 3 should have been Kes in season 6. That would have been a better development for the character. I also agree on your statement that season 3 Kes should have been teen Kes, a little more rebellious and bit more of a risk taker.