The problem was a lot of those fillers in mid-Johto especially were very tedious to sit through, the writers pretty much ran out of ideas around that point and TR began to get stuck in a rut. Sure there was the occasionally really good episode from time to time, but for every good episode there was like 5-6 repetitive/dull eps right beside it. Kanto and Orange Islands are really the only seasons where almost every episode is worth sitting through, even the "weaker" eps those seasons aren't too bad to sit through and since the eps move fast it doesn't really matter with such short seasons.
Even I was watching Johto at the time it was airing, I didn't really remember having an issue with the fillers. Yeah, there were some weak and boring episodes, but that's true for every arc. The slow pace didn't affect my enjoyment of Johto at the time. I'm just not confident that kids watching the show on Kids' WB would really care that much about pacing or if everyone would think that all of those filler episodes were dull. I enjoy the Kanto and Orange Islands sagas too, but I wouldn't put them on that high of a pedestal either.
Also that's where the negativity for the Pokemon anime online began, where people always used to say, "Every episode is Team Rocket attacking the group and stealing Pikachu or the Pokemon of the ep and getting blasted off" or that "Ash doesn't evolve most of his Pokemon," etc. A lot of those complaints were valid back then, along with the lack of any real character development for Misty and Brock. The show was stuck in a rut back then and even when we were kids or young teenagers, we all acknowledged that at such a young age when we were close to the target audience of the show. And while of course every series has fillers like this too, there's at least less of them and more important things happening from time to time.
To be fair, both of those points would easily apply to the Kanto and Orange Islands too. Team Rocketing attacking the group to steal Pikachu and/or the Pokemon of the week only to blast off at the end definitely didn't start with Johto. Same with Ash having unevolved Pokemon. Maybe you could say that those points were more pronounced in Johto due to its length, but saying that negativity for Pokemon online started with Johto is a bit of revisitoinist history again. The anime was repetitive before Johto too.
If anything if Johto was written like Kanto was just with better battles (like Johto at least had), I would have loved it. There is the occasional ep that feels like a classic Kanto ep, "Just Waiting on a Friend" from Master Quest with that ghost Ninetails who thought Brock looked like her dead master...that was a great episode that would have been considered a classic Kanto ep if it took place back then. But since it happened in late Johto a lot of people don't remember it. That ep and the Temacu episode, or the Blissey ep for Jessie, etc. Johto had its gems, but there's just too much repetitiveness there that brings it down. That and of course Ash's Johto pokemon didn't really get the proper development they needed, so you couldn't even get excited to see Ash's Johto team develop because you knew they would only get very little.
I really like that Ninetails episode too. It's one of the better Brock episodes in the original series. I'm not sure if it would have been considered a classic had it aired in Kanto, but it probably would have gotten more attention at least. I'm pretty sure that the Blissey episode is remembered pretty fondly. Most Team Rocket episodes are held in high regards among fans, it was pretty early on in Johto and was referrenced in DP when Brock caught Happiny.
I don't think fans at the time knew that Ash's Johto team would get very little and thus couldn't get excited for them. Aside from Pikachu and Charizard, Ash's Kanto team didn't have a lot of development either. The difference is that they had more screentime to flesh out their personalities. They didn't really do that with most of Ash's Johto team, which is a shame. I love the Johto starters, especially Cyndaquil and Totodile. Cyndaquil was practically his ace Johto Pokemon and really should have evolved after defeating Steelix. Totodile was cute, but battled so rarely. Noctowl had a cool design and capture, but they didn't really make much use of its movesets. Bulbasaur stayed on way too long and Phanpy felt like an afterthought. A lot of this could have been avoided if they were caught at the start of Johto instead of after giving his Kanto Pokemon sendoffs. That combined with how Ash's Kanto Pokemon took center stage starting from his battle with Clair, that really limited how much development his Johto team could have.
This is why I think that they learned from Johto because they gave Ash fresh teams at the start of each series going forward. This didn't mean that all of his future teams were perfectly handled or even better than his Johto team, but giving Ash new Pokemon from the start instead of waiting awhile longer to do so does make a noticeable difference.
