I certainly don't find all of the Johto episodes atrocious. Now that I've ruminated over it, I don't think they're atrocious at all to begin with - I just would say that the ample repertoire of filler material that came midway could have been executed much better above all else. The nature of the episodes doesn't seem to know the cruxes well, or just plain doesn't mesh. Too many of the episodes seemed forced, predictable, rushed, but even worse than that very, very redundant.... even linear (though I feel that intercutting stories can dramatically reduce tension, depending upon how the pace is set). Not only are the episodes redundant, but the characters begin to lapse into a point where they seem to be limited to the same... tendencies they've always been limited to.
But that doesn't make them inherently bad in my eyes. If anything, it was great to see the original, main cast together one time more for me, and the latter portions of Johto call to an epic nature that not even the end of Season 1 did to me (what with episodes like "Rage of Innocence", "Promise is a Promise", "Address Unown", and "Hatch me if you can", amongst a great many others, though I do prefer Season 1... it's just that things were kept a bit condensed so as to build towards the more epic episodes as the series was being introduced). IMO.
Top it off with Ash finally becoming a great deal more mature (much more collected and placid in tone, and a greatly more kind person, as well as being more responsible when it comes to the things for which he is responsible), as well as Misty's departure (which I always find heartwrenching - I feel run through the heart whenever I watch it), and I feel the Johto episodes are rather solidified, even moreso than the Orange Island filler arc. If anything else, if I had to choose an apposite place to end the series, it would have been Johto. I feel the Master Quest season made for a great ending. I'm satisfied with the resulting season(s) as an overall, even given the point to which they went.
I'm not a fan of all of the Pokémon of the Johto region, but I do like a number of them enough (Cyndaquil, Chikorita, and Bayleef come to mind, amongst a few others). But I suppose whether you enjoy the episodes or not just greatly depends upon opinion. It also may tie into which one you saw first - for some, Season 1 will always be prevalent. For other's, it's the new plethora of episodes. That's not the case by full intents and means, though - everyone has their own preferences. But to draw this post to a close, while I find the Johto fillers somewhat vexing, I don't hate the series at large or even dislike it. It certainly could have been improved upon in my opinion, but I still feel they're good when all is said and done.
