Basically the entire of Pokemon went downhill about the middle of Johto, possibly even before (I haven't seen the start of Johto so I don't know.)
Team Rocket had a lot of depth. They seemed like bad guys sometimes, but they had reasons for everything, and there was so much beauty, and drama and things that made you just hang on to their characters and believe that they were good and love them even more.
The underscore of Pokemon for different episodes and scenes really made it what it became a long time ago, and so many fans hung onto Pokemon because it was just so deep and beautiful, and amazing in every single way. And yes, there were jokes in there that either made you laugh or think really hard, like about James's sexuality, Ash's father and Butch's voice (and probably more that I haven't heard of yet) but it all pulled the fans together and made one huge family of fansites on the internet and awesome fanfics that were so dark or deep that they really drew you in.
And there were parts in Pokemon that scared you, or made you cry because the storyline was so sad and touching... but the best parts about them were... like I've just said above.
Unfortunately because Pokemon is entirely about making money instead of the actual depth and proper story to the fandom now, the series has been completely raped so yeah. Team Rocket has gone down as well as everything else. They went downhill a looooooong time ago.
And Pikachu is retarded now it's like level 500 or something, and there are no references back to their old Pokemon, like how much they loved them or were family or whatever. No history for any character now, or beautiful memories for the older, classic Pokemon. Same with Ash's Pokemon. TR's Pokemon just decided to leave them on a whim because of some random guy... which I can't remember much about, except he had a cage or a.. gun or something? The TR Pokemon wouldn't have run away they would've fought so...