A early chapter has Team Rocket's Meowth learn from a female ninja Meowth Pay Day. In a later chapter, we learn that this female ninja Meowth is Meowzie, who is the reason why Team Rocket's Meowth learned to act human.
Team Rocket acting competently. I'm not quite sure why, but given how much of underdogs they were, it's really nice to see them get victories, see them actually on Ash's level, get acknowledged by the Boss as being hard workers...
Chapter 20 has the birth of Damos, the first new Pokemon that Professor Oak has gotten for himself in a decade, whom he welcomes into the world, and his home, in a particularly touching manner.
Mewtwo's reaction to getting his memories back. It really shows how much Ash got to the guy in canon.
Ash got most of his badges the first time around in the tests of Character. It's kind of heartwarming to see the guy honestly winning matches, instead of, say, getting rewarded for saving the gym from Team Rocket.