Originally according to ex head writer and his blogs original trio was intended to be kept as permanent cast in pokemon series.Only reason why Brock left for awhile in Orange Islands was due to initial fear of Brock being viewed as racist stereotype among Americans because of his eyes.
Purpose behind Ash,Misty and Brock being reunited for Johto was because writers figured out due to their popularity how they are working formula for this show,planning to keep them for next series and onward.
However their mistake was that they didnt took in account how Johto was vastly longer saga than Kanto was with popular group not being enough with series requiring little more substance to maintain people interest.
Problem with Johto wasnt in reuniting same group again with original trio already proving to had potential to work as group,but in writers inexperience when writing for long sagas which needed to be stretched out for 3 years or so until new games come out.Johto was their first one with writing staff finding themselves basically in front of wall.
Johto did improved some things like providing better battles,giving little more character development to Misty and Brock,being ground-breaker in introducing mini story arcs which were later expanded on during AG and DP era.That and chemistry between original trio and TR were the only other working parts.
However excessive use of fillers,drop of plots like GS ball,Ash and groups pokemon and goals not being treated well,Ash older pokemon being "released", as well lack of any real rivals with TR going nowhere were reasons why people started losing interest during Johto series.Combination of lack of ex head writer care and writers inexperience in handling some things properly back than were one of main factors responsible for this.
Another reason is because original fad started to die out.
Because of ratings starting to drop and because of third generation coming up with contests,writers decided to add some change in show by introducing new characters.
However only reason why Misty was chose to be replaced over anyone else was because she was girl,being already explained in one of interviews and in ex had writer mr.Shudo blogs why are girls being replaced.
The only reason the original trio was reunited was because everyone raged about Brock being replaced and really disliked Tracey. I liked him. So they panicked and brought back the character they knew had a large fanbase already.
When Misty left this caused even bigger backlash among fandom,so im not sure if fan demand had anything to do with his return.
Writers almost never listen to fan complaints and according to ex pokemon director mr.Hidaka,Tracey served mostly as testing ground to see how Americans react to Brock eyes.After seeing how they had no problem with this with character already being liked,they decided to give him another shot.
It seems to me as if Johto gave people the illusion that the original trio was important. I think this is why some people don't understand why it was never reunited again afterward, it was never meant to.
I dont think you understand how popular during series heyday original group was.They played important role in introducing pokemon anime to million of viewers worldwide contributing to its popularity.Ash,Misty and Brock as group even to this day are still most recognizable and iconic group out there and there is a reason for this.
And during original series original trio was treated by writers as important group,otherwise they wouldnt be planned initially to stay even past Johto.
I gather how reason why many people still think how original trio might be reunited again was because of still having potential as group which is self explanatory considering how they werent fleshed out a lot,because of being most iconic and recognized group which made show popular in first place and because of high demand and popularity.
In most shows first set of characters is usually most recognized and iconic,being responsible for anime becoming popular in first place.As such its almost always guaranteed how they will never be forgotten just like first generation of games wont always having chance to return because of this.
For that reason alone people still think we might see first group reunited again,making actually sense if it happened in final saga or something.Since it would emphasize better on closure ad anime coming back full circle since it would end with group which started it.
All Johto serves as a reminder of now is why the show kept changing after it ended to better suit the series.
Show keep changing because its nothing more than tool to promote new games really not having consistent and well developed storyline.If contests were introduced in second generation of games Johto would probably be largely different than it was even if same group still stayed.
The reason why they keep changing the characters is to give the series a slight ratings boost at the beginning of each saga.
Except thats not really a reason,considering how return of popular and liked older character would also give boost to series with people viewing it as nice twist to current formula judging by demand.Reason why writers rather replace characters with new ones is to provide new fanservice(or "eye candy")according to mr.Hidaka and his interview.As shallow as it may be,there arent any complex reasons behind characters being replaced.
EDIT:
That's the thing. It's too predictable that they're going to change the characters every saga. Was the decline in ratings for Johto that bad? *rhetorical question*
Interesting thing is that at times AG had lower ratings than Johto did.According to some sites Johto generally had higher ratings than Battle Frontier did.
In reality only reason why Johto wasnt successful like Kanto was because of poor writing and lack of writing experience in handing some things.They had popular cast,popular pokemon and workable chemistry but they screw things up by wasting much of potential on too many fillers from which no one benefited.
However contrary to some belief Johto did some things right having several great episodes giving some notable development to characters having certain charm(at last among main group and TR).It wasnt trash like some pretend to be the case.
Personally im so so about this region,not being my favorites nor worst region.