I struggle to say the world is darker, but more so the theme is meant for Young Adults or Adults, whereas the Anime, Games, etc are meant for Children. The Anime and Games are dark but aren't framed that way so it gets brushed over or laughed off. Alongside that, more realistic things that were later dropped into the Games or Anime over time are here from the start.

Brock's main Pokemon aren't some untrained Geodude and an Onyx. He has a real, and strong team - he just doesn't use them against some rookie with no badges. This is just one example.

The world isn't just in harmony with completely open borders, everyone going wherever they want. No, there is political tension, there is struggle. After all - if the world was perfect and all Nations allied, how in the ever-loving Arceus would Criminal Organizations that could affect or even destroy entire Regions even exist? How could you ever gain any true tension?

In canon, I believe it is said that Koga trains students, and those are his Gym Trainers, well. It's a clan here. Think Wataru, Draconids, etc.

Everyone is born with Type Energy (Aura falls under this as a more special version, not very relevant.) Some people are born with one, limiting them to 'bonding' with that type of Pokemon, and Normal types. Some are born with two, or even three types. Some - those lucky few, can bond with all Pokemon.

When bond is mentioned, we aren't simply talking about becoming friends, but a metaphysical bond between Trainer and Pokemon - a symbiotic relationship where they give and take from each other, benefitting both of them. The invention of the Poke Ball allowed trainers to form this bond significantly easier, alongside making it even possible to train Pokemon outside of their type - albeit truly bonding with them is highly unlikely, albeit not impossible.