I can't help but think that the writers never really liked having Misty in the series. As someone who has watched most of every saga of the series, this is why I think this:

1. Misty was the first classic Kanto character to leave the show. Ash, Brock and Team Rocket all lasted in the anime for 13+ years, while Misty was dropped way back in 2002, back when the anime was still at the beginning of its lifecycle. She was officially the shortest-lived classic Kanto character of the series.

2. As we can see now, Misty's departure at the end of Johto was indeed quite permanent. Misty stayed gone permanently for the entire duration of the series and was never allowed back into the main cast in any of the following arcs.

3. Misty's cameos/guest appearances originally stopped as early as 2005 back in mid-AG, and the writers didn't give her another appearance for a whopping 12 years till recently in SM for the 20th anniversary. It seems the writers were "done" with Misty after Hoenn ended because that's when her cameos stopped, and why they didn't even bother bringing her into the DP series at all. If it weren't the 20th anniversary in 2017, most likely she (and Brock) would not have appeared in SM either. If you don't count stuff like flashbacks, Misty missed 3 gens in a row and over 12 years between appearing. It seems like they "Tracey'd" her.

4. All the biggest water-related plotlines in the anime happened after she left. Hoenn had Team Aqua which was a villain team all about water. Movie 9 was a blatantly water-themed Pokemon movie with a legendary who was the "prince of the sea." Wallace appears in the DP series as a, "Water Pokemon Master coordinator" and Misty doesn't get to meet him. They gave May blatant water-themed plotlines instead of using Misty for them. Dawn gets a Piplup which was the most heavily promoted water pokemon on a main cast member outside of Ash.

5. Dawn got a Togekiss. Back at the start of the anime, Togepi was exclusively associated with Misty and no other character ever had a Togepi in fillers in the series. Then instead of Misty reuniting with her Togetic, the writers decide to debut Togekiss with Dawn instead.

6. She was probably the worst treated of all the female leads in the series. She barely got much screentime and was always kept on the sidelines while Ash did everything. In many ways May, Dawn and Iris all got bigger roles in their respective sagas than she got, making it seem like Misty wasn't very important.

7. Misty did not get an ending theme in the Japanese version of the anime, while other female leads did (May, Dawn and Serena)

8. The writers dropped Misty the first opportunity they got, which leads me to believe they might have dropped her at the end of Orange Islands if a female lead from the games existed with G/S instead of Crystal.

10. She's the only pre-SM female lead with no ongoing rivals, unlike May/Dawn/Iris/Serena.

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.

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.