I would choose no one?
None of alternatives we had like Casey, Janine or game heroines(Marina from Crystal) would have been viable choices or have required stamina and potential to bring same level of entertainment value, impact on plot or potential to advance forward like Misty did imo.
Even more in Marina case since she wasn't created until mid Johto when series on good part were already unfold out having planned route and way in which things will play out regarding plot and characters.
Needless to say im glad Misty was used for Orange saga and Johto instead of leaving after Kanto which would have been incredibly short run. Liking her sarcastic,witty and spunky type of personality developing in more mature and level headed character over time finding right blend of tomboyish and girly side. She made this show more funny, endearing and meaningful having that deep and entertaining chemistry with group contributing to quality character interaction. She left huge impact on Ash development as trainer teaching him about basics, how to not rush in danger, provided needed encouragement and push to others to train and nor back down.
Along with contributing a lot to plot and way in which series would play out admiring her aspiration of striving to become master of water types, various fears, sad past and flaws, strength and interesting pokemon she had.
If anything instead of removing Misty for Johto i would much rather prefer if writers added additional girl to main cast in Johto series. In case anyone remembers Sakura(girl with Eevee, later Espeon which became recurring character appearing in hosos too).
Misty even invited her to join cast. Having excellent interactions in their girly talks, ability to relate themselves to each other over older siblings and issues they have with them, funny scenes full of humor and quirky behavior etc. Which would add breeze of fresh air in main group during Johto by having two girls in same cast, something we had to wait unfortunately for more than 16 years to happen.
Needless to say during time Misty was in cast whole idea of constant girl changing wasn't even established yet. Originally going by Takeshi Shudo ideas pokemon intended to have permanent female in cast just like Ash treating anime as continuity based show which buils on story, friendship and development of its characters exploring them to deeper level.
Sole thought of starting pattern of constant girl replacing didn't even came to writers mind before Hoenn, which in my honest opinion proved to be cardinal mistake denying this show of continuity, properly fleshed out characters who leave inadequatelly explored and stable story.
Which was apparent with Misty character too leaving cast without being fleshed out enough with many things being unexplored (like her past, goal of water master, desire to become water expert proving herself on global level reaching E4 strength like its case with Lorelei, relatives, underused pokemon team and issues,fears she still has which could be used for much more development)with no further going forward or direction ever happening. Taking with itself away strong identity, charisma and lively atmosphere she brought .