I'm sure a lot of people would agree with you, given how much people express annoyance with them. For me, Team Rocket has always been my favorite characters, ever since the beginning. Unova went and turned them into completely different character, removing practically everything I enjoyed about them in the process.
I can accept that you like them, and I'm happy for you that XY brought back who they used to be.. at the same time, why does it mean they have to be shoehorned into every episode, even ones where they wouldn't fit into the plot? That's the part that I don't understand about what you're saying you're wanting.
For example, and you may not have heard of this show and that's fine, but there's a show based on Archie Comics that debuted last year on The CW called
Riverdale and it's had two seasons. My favorite character is Cheryl Blossom. I like many things about her including how she looks, her behavior and attitude, the storylines the writers give her, etc. At the same time, there's so much going on in the show that I accept that she can't appear in every episode, and I'm totally ok with it. I appreciate that they don't try to shoehorn her into episodes where the plot would make no sense to shove her in. So I guess coming back to what you're saying, it confuses me that just because you like them, you think they should be shoehorned into episodes where they contribute little to nothing.
A good example is Korrina's gym battle. You like Team Rocket's bumbling personalities on a weekly basis. That much is clear about "my favorite characters since the beginning." Do you feel their 2-min appearance, with Serena and Clemont quickly dispatching them, did anything to entertain you or display their character traits that make them your favorite characters?