Team Rocket never got a proper resolution.
Team Magma/Aqua arc started okay. Despite being cheesy, it was rather self-aware of its cheesiness. The final "fight" was extremely boring though, it truly brings down the entire arc's ranking by a lot.
Team Galactic arc was more serious, but their episodes were too spread out, the finale was anticlimatic and i feel like the admins were rather underwhelming compared to Hunter J.
Team Plasma was unfortunatelly robbed of a proper introduction due to external factors and because of that they lost some of the most interesting moments from the games. They had to somewhat adapt BW2 (very loosely), which was... okayish i guess. Quite cliché, but to be fair all of them are (like literally every single one of them). Wish the whole discussion about the ethics in battling pokémon was more developed and that the other characters besides Ash had a bigger role.
Team Flare was also cliché just like the others, but i don't have much to complain about the execution, since they took the team seriously and had some amazing action scenes, with all the characters playing an important role. I also liked how the admins didn't hold anything back just like Hunter J, being just as cold and cruel as her. The whole Megalith thing was very weird, but i guess at least that part wasn't predictable.
So my vote goes to Team Flare and Hunter J. With TF being first and Hunter J second.