Best: Move differentiation. Pokémon deal damage based on their attack or special attack stats. Before Diamond and Pearl, these two were tied to types, with more elemental type moves (fire, water, grass) dictated by special attack, and more tangible types (rock, steel, fighting) dictated by physical attack. In other words, if you had a grass-type Pokémon with high attack stat but special attack in the basement, they were functionally useless on offense. Diamond and Pearl made it so specific moves, rather than the types they were affiliated with, were characterized as physical or special attacks, instantly turning a wave of useless Pokémon into unstoppable battle machines.
Worst: The stakes were too damn high. Pokémon games always cast you as a young trainer on the quest for being the (very) best (like no one ever was). Ruby and Sapphire upped the stakes a bit by introducing legendary Pokémon who could cause severe regional flooding or droughts—extremely bad, don’t get me wrong, but not exactly Thanos-tier stuff. Pokémon Diamond and Pearl, however, kicked things up to 11 with legendary Pokémon who could shatter time or space, plus a literal god Pokémon who’s responsible for all of creation. This is where Pokémon’s narratives started to fully jump the shark.