I can't help but think the writers never cared for Misty much at least after Orange Islands, while every other female companion gets better treatment than she did:

May is the first female lead from the games and is thus given the biggest role in the show for a main character at that time. The Contests get treated as seriously as Gyms do and become a huge arc across the series. May is the first actual well developed character of the show who essentially turns out to be one of the better battlers among the main cast. May's popularity was one of the initial reasons the writers moved on from Misty.

Dawn was basically the writers using May as a template and going further with it. She's treated as even more of a co-star, gets the most amount of screentime/episodes of any female companion past or present, and gets the closest to accomplishing her goal of any character.

Iris, while not being handled as well as May or Dawn, is given a Dragonite which is unthinkable for a main character, and then goes on to meet Claire in Johto.

Serena has a canon crush on Ash, the first girl since Misty who is obviously into Ash. She gets a childhood backstory making her the first girl to meet Ash over Misty, and her crush on Ash is brought up quite a bit to the point that they're making a psuedo-date episode. With the writers giving a new girl such an obvious crush on Ash, Misty's crush seems to be a thing of the past.

Lastly Misty herself hasn't appeared in ages. She left the series back in 2002 a whopping 12 years ago, and her cameos never continued past Hoenn, so Misty hasn't even shown up in an episode since 2005...which by next year will be a decade ago. Misty hasn't had a single appearance outside of flashbacks in nearly a decade, let that sink in.

You could arguably say the writers turned the series against Misty in almost every way possible. She was treated almost the same way Tracey was after he was written off.