The main problem with Johto fillers were that the plot was several times this:
Ash & Co. meet Cotd X.
Cotd X needs help from them.
Ash & Co. start helping Cotd X.
TR comes and ruins whatever Cotd X wants/needs.
Pikachu Tbolts Tr who blast off again.
Cotd X finally achieves his dream/goal.
They live happily ever after.
Arguably ill say Johto episodes contained more emotions to it imo than DP ones. We had several ones where characters experienced breakdown or tragic incident occurred. Such as "Ignorance is Blissey"showing us sad, touching backstory of Jessie trying to become pokemon nurse. "For Crying Out Loud"where Misty saved Marill life developing strong bond with it with sad heart having to let it go. "Joy of water pokemon " where Misty burst into tears when nurse Joy crushed her childhood dream of examining water types. "Bulbasaur Ambassador" where Bulbasaur tried to saved Oddish almost getting killed. "Charizard Chills" where Ash send Charizard to special training etc, etc.
And of course who can forget "Gotta Catch YA Later" which was one of saddest and most emotional episodes ever in my opinion, being saddening to see group which passed through so many things together becoming great friends having to split up.
Of course that JOhto had episodes you mentioned following formula of helping COTD about their problems, but honestly so did AG, DP, BW and even Kanto.
There were many episodes which didn't followed this pattern breaking out of mold such as: "Ring Masters" where Ash Snorlax fight Feraligator in sumo match winning first place, "Unbearable" where we had evil Teddiursa stealing pokemon food with Misty being guillible falling for its charm, "Sick Daze" where Ash and Misty had to do Brock chores when he was sick revealing how they are terrible cooks and rather disorganized showing how desperately they were dependent on Brock.
Mini competitions like one about extinguishing fire where Ash participated using Misty pokemon with Psyduck ruining everything, "Bug catching contest" which granted wasn't any special but Misty interactions and panic fear from bugs hitting everything left and right making episode worthwhile. Etc, etc.
And out of those which revolved around helping COTD good chunk was actually interesting imo. Like one where Ash Heracross battled Scizor, or Bulbasaur battling Hitmontop. One where Misty argued with fire trainer Egan due to her Poliwhirl failing in defeating Macargo, revealing why she likes water types giving her some good growth in character sense etc.
Looking back i actually think Johto had several memorable, interesting episodes which contained development for main characters and TR having more to it than just gyms and league with people often overlooking it focusing mainly on bad sides.