I didn't like Johto much, not because of the fillers, but the entire saga was almost a copy and paste of Kanto.
What I did like however is these things:
Whirl Islands Water Pokemon Tournament - I just really enjoyed watching it and then Ash and Misty battling.
Team Rocket - Team Rocket had a much more substantial threat level. Whirl Islands, Lake of Rage... I love almost every episode where the real Team Rocket was in it, not just the Trio.
Gary and Ash maturing, especially Gary. I hated Gary in Kanto, but he was amazing when he showed up in Johto, but I think he should have showed up a lot more.
Silver Conference - To me, I think this was probably the best Pokemon League. The battles were epic and meaningful. I didn't even mind Ash losing to a brand new character because the battle was so amazing.
Cassie - Forgive me if the name is wrong. I loved Cassie's character. She was a Tom Boy, but she was still a girl. Her character was awesome. And again, I just wish she had showed up more in the anime. She is also the only trainer Ash upright gave a pokemon to. Though you do have Primeape and Haunter, but it wasn't like the Beedrill.