No one is without flaws, so among my favorite characters its undeniable they had several weaknesses leaving a lot more to be desired.
To name some:
Misty: she may be my top favorite protagonist from pokemon series but I do wish she rained her pokemon more on screen. Granted that's writers fault, but still seeing her do visible training not related to Togepi and Psyduck would had been very much appreciative.
Her temper as adorable as it could be did sometimes crossed the line dishing out more harsh words and actions than needed toward other characters not recognizing that herself. However to be fair she became more aware of her flaws and open to different opinions later on.
She should had received much, much more focus in Johto than what it came down to in end having enough life left in herself, potential and interesting things to warrant staying as main character.
At very least for whole AG generation given how heavy water centric it was offering ton of new water pokemon, specialists like Wallace and Juan from who she could learn more innovative techniques. Hell villains Team Aqua connected to legendary Kyogre were perfect opportunity to have water enthusiast and someone who devoted himself to become water master to be involved in whole thing trying to stop them.
Bottom line Misty received short end of stick with her status as main character ending prematurely.
May: she could sometime went overboard with whole crying streaks pitying herself when falling under Harley tricks or losing contests.
I mean its ok to feel let down and disappointed when something you invested into so much don't pay of, but this happened a bit too often for my taste wishing she learned how to suck it up and become more strong willed of character.
She sometime lacked creativity in her appeal rounds feeling abit bland and predictable after some time. And while i enjoyed her more straightforward and direct trainer battling style under Ash influence for her profession to did her eventually quite a harm.
Ash: I like this guy but he is unfortunately pretty dumb, and his lack of knowledge or fact of being incredibly dense can be highly irritating at times. Even for most obvious things like TR setting up trap through his friends could see through with no problem(special mention to Misty who was more skilled in that than any other companion).
Or girls clearly showing signs of romantic affection, sometime even not noticing clear signs of what his own pokemon want making fool out of himself.
Ash can be genius in battling with pokemon, trains and work hard. But he became over the years too accustomed with strategies and moves which work for agile and fast pokemon. And he makes best results with speedy pokemon being in his own element.
But as consequence heavy, bulkier tank like pokemon are his Achilles heel not doing much research and preparation to develop effective battle style for them. And it was showed best with Torterra in DP how he should be more versatile as trainer. Not relying only on certain pokemon that much.
Ash neglects his friend. I know its writers fault obviously, but way things are depicted. Never calling or checking up on May, Misty, Cilan, Brock, Dawn etc. Hardly ever visiting them etc gives impression of not thinking much about those who helped him to evolve in trainer and person he bis today or don't care much in general.
I know that's not true, but it seems that way.
Brock: deserved more screentime, character development in general.
His approach toward girls and women in general is wrong and after some time became more tedious than funny. And I wished he battled more because he has lot of impressive pokemon and interesting battling moves.
I love ya, Misty, but after Kanto you did so little you may as well have been a recurring instead of a main one.
To be fair that's fault of executives meddling in writers plans(something mr. Shudo in blogs made rather obvious) and anime being in early stages still not being even decided its faith, let alone direction of characters.
Still Misty almost shared focus and attention equally in Orange Islands being incredibly active there. Heck she managed to even overshadowed 2 of Ash gym battles with whole Danny and Rudy flirting games and playing hero in saving sister from one of them life.
In Johto you have a point though not fully because in Master Quest Misty really SHINED. Whole Whirl islands detour and in general whole season gave her lot of quality spotlight.
Heck, even in mid-Kanto she lost her mojo after she got the soul stealing egg beast...
Ouch, that's harsh. Togepi was just fragile baby needing someone to take care of him, And this did helped Misty to mature and become more compassionate as person allowing for one of most emotional and well done goodbyes in pokemon in Misty first Hoenn cameo. Giving both some nice character growing.
Most importantly i don't think Misty lost her spark and soul. I guess you could say she was less violent but that's understandable since she matured, though still showing lot of spunk, passion for various hobbies having competitive flare and passion.
She often ignited reaction from Ash side with snarky remarks and annoyance and better balanced out Brock eccentric personality having more memorable friendship with all companions in main cast than any other imo. On top of that i enjoyed in healthy mix of prideful and mature, yet tomboyish and quirky side bringing more humor, tension and fun dialogue between characters in unforced, spontaneous manner than Iris did for me seeming to develop stronger friendship with her friends.
Still seeming highly passionate, snarky and with life in her eyes in late Johto, chronicles and recently SM episodes.