Do you mean what seasons of the show did I like? Or the generation that was showcased for those collective seasons, like Johto being for "Johto Journies", "Johto League Champions", and "Master Quest"? Because it isn't really good to lump them all together. As in my opinion, Johto had some major weak points in terms of plot and writing. (See answer below.)
Because each question has a different answer. I'll just give both.
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So far, I have to say that the first generation was the best. To watch little Charmander evolve into a big bad Charizard was a treat. It was also great to see how Ash coped with learning that not all Pokémon stayed the same personality-wise. This was also when the Pokémon had real personality. Pikachu actually left Ash's shoulder to do more than the random Thunderbolt to save the day. Bulbasaur set the world on edge when he refused to evolve on his own decision. This was really the generation that had few faults being shown.
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The worst season, without a doubt, would be "Johto League Champions". Filler upon filler upon filler... There was no break between one random trainer to the next. And they all basically had the same problem that was solved the same way: lack of confidence; beating Team Rocket. Gyms were dozens of episodes apart, and Brock and Misty were sent sailing into the background of cardboard-dom.
While I particullary enjoyed "Master Quest" for being the last hurrah for Misty and Gary as characters, and a certain character showing up for the last six episodes, it was still with the occasional filler.
In my opinion, the first season with May, "Advanced" was the best, from what I have seen so far. It was fresh, and had gone back to the days of old. Ash was just "starting out" again, and there was a new trainer on the block. We learned along with May about the new Pokémon and about the world. It was interesting, to say the least/for lack of a better term.