With no further adding,Johto was treated more like continuity from Kanto and OI than anything else.After Tracey fiasco and after witnessing how their initial fearing of Brock being viewed as racial stereotype because of eyes was ungrounded,writers decided to go back to group which started series already proving to be well liked and proven formula.
Initially it was planned to keep Ash,Misty and Brock as group permanently in series from there and onwards,but after ratings started to drop due to poor writing and pokemon fad starting to dye out writers changed their mind and opted for adding some change in cast.However in longer run i think it would be more beneficial for anime if formula was changed by not necessarily changing main cast.Like shaking up dynamic by adding fourth character or replacing TR and current story taking group in new direction.
Speaking of Johto,Master Quest was probably best season not falling in quality behind AG.For start number of pointless fillers decreased significantly,Misty and Brock(to lesser extent)received more focus,there were several arcs introduced which contributed to current plot(Like Whirl Cup,Red Gyarados,Lugia,Larvitar etc),gym leaders were depicted in better light(like Pryce and his past or Clair which pulled with itself mini arc about Dragonite)group pokemon started to gain better development(evidenced by more evolutions,captures and change of attacks in their roasters) along with Johto Silver Conference being pone of best leagues we ever had.
However i wouldnt say 3rd and 4th season didnt had worthwhile things because they did.Several of fillers were rather entertaining and unique,some past characters from Kanto appeared(Like Duplica,Todd,Aya or Suzie)being nice throwback to cast,there were couple of recurring and amusing pokemon(like Jigglypuff,Snubull and later Delibird),Ash companions got some valuable development,battling overall got improved and original trio was still good feeling like genuine group of friends having good chemistry and several memorable moments.In fact Ash,Misty and Brock dynamic and Jessie,James and Meowth comedy were saving grace for several of those fillers becoming watchable compensating for poor writing.
Granted our heroes often stood in background in episodes which revolved around COTD and helping their pokemon,but when they played some role and got focus they were delivered as enjoyable group having same spark they had in Kanto.
For that reason alone i cant pick on original trio for this because reason behind poor quality in some episodes was due to characters being neglected.
Anyway, im going off an a tangent, I still dont see why everybody misses Misty, she just got plain annoying towards the end, teasing this love for Ash which never really got any further development, dreaming of becoming a water pokemon master but seldom adding any pokemon to her team, I mean, Psyduck for instance, one of the main pokemon in her team that got any attention basically got dropped.
People miss her from what i noticed because they find she had enjoyable personality providing best dynamic within group so far,gave identity and humor to anime,because she wasnt developed to full potential never getting any real closure and because she had interesting backstory and past finding character deserved better than what it got in end.
Of course whether someone is interesting or prominent is matter of personal perspective but after seeing how unfairly character was really treated i can see from where theyre coming from.
People often say Misty and Brock should've been replaced with Gold/Kris to promote Johto. Why would they put themselves at risk again with another Brock/Tracey fiasco? And who could possibly fathom the potential backlash had they replaced Misty before Johto?
Thankfully writers dont listen to fans.There was no reason to replace Brock and Misty in Johto at all,and after realizing how successful and popular original trio was writers probably figured how best move would be to use already proven formula.It was their fault and mistake for dropping ball and not utilizing group and Johto to potential it could have,because good group wont get you far if you dont treat anime plot and story properly.
As for Misty,actually her departure caused backlash after Johto as well.I remember complaints being higher than it was case with Brock.