Max just wasn't handled well after early Hoenn, besides that one Ralts episode. Bonnie was a little kid companion character done right.
As for me:
Johto: All the Team Rocket fillers were gold. It's amazing that as dull as most of Johto was, all the Team Rocket/Wobbufett eps are the funniest eps of the series. Of course the league at the end was great too.
BW: I actually loved the Don battle tournaments, some of the secondary rivals, and the beginning was ok. But sadly BW falls apart as it goes on. I don't think BW is completely terrible, it has it's share of good episodes, but when you think of the saga as a whole it's just so lackluster and disappointing.
I'll give credit to both Johto and BW for handling TR in a way that didn't feel tacked on, which was rare for most post-Kanto parts of the show.
Johto was still revelling in having them as pseudo villain protagonists, still calling back to their backstories and complexities and keeping their jaded chemistry with the twerps. Also liked Wobbuffet having more involvement in the schemes in this era, even SM despite having him out of his ball full time doesn't actually let him do much individually (if I remember correctly Likitung also appeared a bit more commonly here before getting replaced as well).
Also Johto was probably the high point for the English dub, the scripts and acting were at their funniest here.
BW was also the famous 'competent Team Rocket' arc, with Giovanni and the whole organisation being an active threat in Unova and the Trio being an actual menace. I feel this would have been much more appreciated if there was a proper transition, if they had kept more of their personalities and we saw them DEVELOP their resources and competence, but all the same it was cathartic to see Team Rocket force proper two way fights out of the twerps instead of effortless beatings, to actually make Ash and co ACKNOWLEDGE THEM AS A THREAT. Even the times they reverted back to being comedic seemed to bring back more of that old rivalry, with more OS level chemistry or creativity like the Meowth turns good arc or some of their DA schemes. This was about the one series TR actually got something of creditible 'final stand' with the main group instead of one final slither of a curbstomp.
Basically to make up for the poor handling of the main arcs, these seemed two rare series where 'Ash vs Team Rocket' seemed an inherent drive to the show and even one of the best factors about it in a way that didn't feel like an insult.