Gee, you do love your Kes, don't you? She was so good and interesting, and so developed and universally loved that they eliminated the role and dumped the actress. What idiots! Wait. Here's an alternate theory: She was boring. Her relationship with Neelix didn't work, and IT was boring. Her relationship with Tuvok was boring, and a waste of Tuvok's screen time. They tried to re-invent the character twice, and she was still boring. They struggled to find things for her to do, and when they did, she was still boring. And because the idea is to attract viewers, not bore them, they dumped her, and replaced her with a character that was not boring.
And they would have done it to Beverly Crusher too, but luckily for Gates, her replacement sucked even more than she did.