Well we know her sisters are never going to take over the Gym, that's pretty certain.
As for Misty traveling, I'm sure she has her, "off days" where she closes Cerulean and travels around Kanto a bit for whatever reason.
Misty sisters already took care of gym before when Misty traveled with Ash.If writers decide to bring Misty back substitute at gym wouldnt represent much of problem since they could easily have her sisters who are still technically gym leaders to jump in.
If anything Daisy showed to spend most of time with Misty at gym showing interest in battling like "Luvdisc is a Many Splendored Thing"showed for example.
Writers could go further making her responsible enough in future to take up gym for certain period of time while Misty is absent.
I don't think it was so much making up for her lack of development but rather the ease of giving her development when she had legitimate problems, such as taking up responsibility for the gym, which is so much easier to convey than her goal of being a Water Pokemon Master.
Problem is Misty unlike say some other characters like May never got any closure. She never achieved her dream or came to some significant realization that will help her achieve her dream. Sure, May didn't win a GF, but she realized that she was too reliant on Ashs training style, set out to establish her own, traveled on her own (or with her rivals), overcame her fear and loathing of Pokemon, etc. She had massive character development and proper closure. Misty didnt.She didnt choose to stop traveling with group nor hard interest in running gym.
Furthermore specials after departure didnt offered any progress of plots of her story(like her goal of becoming one type master,to learn everything she can about water pokemon,other aspirations etc)nor there was ignited any change in character of deciding to pursue something else.
We all know how whole reason behind taking over gym and staying as because of incompetent sisters(not having anyone to rely on).Similar how Brock had drams of becoming est breeder but took care of gym before he met Ash because of not having anyone to rely on.
Half of her initial roster was crippled due to the inability of working well on land.
To be honest problem wasnt so much in their inability to battle outside of water but more in fact of writers treating some of her pokemon poorly not giving them deserved development.Take for example Goldeen.Writers had several opportunities to make good use of this pokemon when group traveled through Orange Islands,in Johto which was riched with water based areas(like Whirl Cup,Seaking competition,all kind of lakes)but they mssed onm every opportunity leaving this poikemon to rot in pokeball being ver rarely usyed.
For this was mainly responsible their incompetence and poor writing.
There were no qualms of evolving it once Misty had run her course and they were probably thinking of some way to give her reason of going to Hoenn. (still felt contrived though)
Not so much.Its clearly obvious that writers didnt developed Misty as much as they could have leaving many thing in her story unexplored and untied.Whole goal of becoming water pokemon master was barely touched on.Whirl cup was good for a start defining whole thing abit but it was too little and too late.Motives behind Misty desire to use only one type becoming best with them were left unanswered(something they exploited in May or Dawn case),We didnt see Misty overcoming her personal issues which stand on her way never coming to significant realization how to achieve her dreams either.We dont know much about her background(like from where fears like bugphobia comes from,what happened with parents etc).
No one can deny that Misty didnt got enough focus.
They could have her back for something else in Hoenn like water tournament with purpose of advancing her goal but they chosen to evolve Togepi over anything else being their priority.I say reason was probably mix of what you and Cyber said.Writers probably wanted to use him for purpose behind Misty return in Hoenn but at same time this was probably their way of developing and wrapping up at least something in Misty story on which they didnt focused much when she was on cast.
I'm basically saying that Misty received better treatment with her post-show than the others in the main cast where their specials could be considered something else.
In other words, I wonder what May is up to.
Well May got some development when she return in Sinnoh too.Her pokemon evolved being showed that she made big improvement in her quest of becoming top coordinator with special showing that she developed her own style as coordinator not being influenced by Ash battling style like she used to be.
Dawn in her DP special after departure managed to get over any possible issues she had with her mother Johanna showing that she developed in mature and self confident coordinator finding in herself strength which she lost in first half of Sinnoh.She also decided what to do with her life setting of on Hoenn journey revealing that her idol is Wallace.
I agree Misty got some great development in specials after departure but to be fair others like May receive some great development too.
p.s.
If you ask me, Daisy could be a possible candidate for taking over the gym, she's the only sister is the most of the time, and she does show an interest in helping Misty. If the writers gave her a little push, she could take over for Misty, unfortunatly I think Misty is too involved with the gym now to leave.
Pretty much this is what i tried to say,.Problem with gym substitute could be easily solved allowing MIsty being free to leave to learn new things and impove as water trainer dpoing steos forward in her goa of becoming water master.
Judging by some episodes in chronicles like "A Date with Delcatty" or "Real Cleffa Hanger"it was showed how main reason behind Misty stay was sisters incompetence complaining for not having someone trusty enough to leave gym in his hands while she is absent.
I could see Misty leaving gym in future following Wallace footsteps to improve and gain more knowledge and experience.
If anything making her E4 member one day would basically man achievement of her dreams since people at this position are best one type trainers in world.
