It has to be Meowth. I don't really know why, though. As a kid, I didn't pay him much mind. When I finally decided to watch Pokémon seriously, from start to finish, a year or so ago, it was mainly because of Team Rocket and because I saw a post on Tumblr that made a joke about Meowth lol So, maybe you can say I started watching with a bias.
And yes, the main reason I watch the anime (even to this day) is Team Rocket (trio). That's why it bugs me they don't appear in every episode now. For me, there was nothing broken about the TRio in Kanto, Johto, Hoenn, or Sinnoh. I enjoyed every minute they appeared in, and I hated what they did to them in Unova. They didn't fix them (there was nothing to fix), they broke them for real this time. And when they attempted to return them to the way they were in Decolora Islands and in Kalos, they just weren't the same. That's when they started to feel tiring to me, like they weren't genuine, original or as funny anymore.
Still, I kept loving those three, even through the worse of times. And I still do!
But, of course, given Pokémon is such a long series and has a rotating cast, there are others I could classify as my favorites too! (Although, I don't think I'd keep watching Pokémon is my all time favorite character wasn't a part of the permanent+main cast —which consists of Ash, Pikachu, TRio and Wobbuffet—)So the list would go like this:
1. Meowth
2. Jessie and James
3. Dawn and Piplup
4. Cilan