I watched every single episode of the Indigo League all the way through the end of the Hoenn saga. I stopped watching at ''The Scheme Teem'' and have never watched any episodes since, so I cannot judge the other arcs, although, they do look a bit worse than the ones I have seen. My favorite would have to be the Indigo League.
1. I grew up with this season, as well as all the original 150 Pokemon. I got a Gameboy Pocket and Blue Version, as well as some packs of Pokemon Cards when I was 8 years old. I started watching the anime ever since the first episodes in America, and I was hooked.
2. I love the trio of Ash, Misty and Brock. I don't like how they switched up the group almost every season, but did not replace Ash or Brock (he was only absent for Orange Islands and Unova). I would have rather had them replace all main characters every time or just keep the original trio, exploring each new region together.
3. I loved how the episodes in the first season had a LOT of Japanese references and the animation was basic, yet very good IMO. I don't like how Pokemon has become overly Americanized with the anime. The games have essentially stayed the same, not sure about the TCG because does that still exist?, and the anime has just changed a lot.
4. The raw emotion of the characters and Pokemon were incredible, which was lost in later seasons.
Honestly, I though the Orange Islands arc was pointless and I did not enjoy really any of it, except for maybe a few episodes. It was basically an entire filler season, while waiting for G/S/C to be properly introduced. It's evident even more so because there have never been a mention of The Orange Islands in anywhere else except for the anime, which bugs me.
The Johto arc had it's ups and downs. At first, I thought it was going to be awesome, but there were SO many fillers, and pointless fillers at that, that it kept be very bored and uninterested. It dragged out way to long honestly. I did like some of the battles and Johto Pokemon, and the Silver Conference was pretty cool as well. Charizard VS Blaziken was epic. Overall though, too many fillers and the character and plot development was very poor. If there was ever a stale point in the anime, it was Johto.
The Hoenn arc was actually awesome IMO. I loved the R/S games, and I thought it was awesome that Ash basically started over and left all his Pokemon from Kanto/Orange Islands/Johto with Oak, and started fresh with only his starter Pokemon, Pikachu. It felt like the very first time Ash left Kanto with only Pikachu. I liked how he had to capture all new Pokemon and build and raise a team. I loved the clothes of Ash and Brock in Hoenn as well. Brock returning after only a few episodes into the arc was a good move, and I loved how he left all his Pokemon from Kanto/Johto behind and only took Forretress. Max was kind of annoying and pointless most of the arc, but he didn't bother me that much. May was cool, and I loved how Ash fried her bike in the first episode, like he did with Misty in the first episode of Pokemon. The battles were awesome, and I loved Ash's team this season, which may have been the only time I ever liked his team. I think it's lame to have Ash always get all 3 starters, and Hoenn was the only time that he didn't. The gym battles were all good except for Roxanne, IMO. The Hoenn League was decent.
Overall, I think the Anime's biggest downfall is that it is never-ending, because with each new Pokemon region introduced in each new game, the anime will follow. I feel like they need to get rid of Team Rocket completely, I cannot believe how they never have been replaced, and I can't believe how no one is sick of them. I don't like how Ash apparently does not age at all, he was 10 during the very first episode where he left Pallet with Pikachu, and he is 10 during the Unova saga too, apparently. It just makes it seems that the anime has no real story, like it's just there to make money or they are afraid to cancel it, ever since the start of Advanced Generation, it just seems like they are wiping the slate clean with each new region and forgetting everything from past seasons. I also refuse to watch the horrible English dub for Pokemon, so I am sure it's even worse in America nowadays.