I've only read any decent amount (so far) of RBG, Yellow, GSC, HG/SS for Adventures, but I always did enjoy the manga even as early as finding some stray chapters in a compilation book in the 8th grade.
Besides the discussion of the manga being willing to get a bit darker with the subject matter without outright veering into dark-edgy territory, I also just think the way it's structured handles how I'd want a cohesive Pokemon World in non-game fiction to be portrayed.
First off, the series is willing to change protagonists after a region has passed. The characters are allowed to actually complete their arcs and mature since the next generation will have a new character rather than the old ones having to become noobs again. One of my problems with Ash is that despite the accomplishments he has made, he barely feels like he changed at all as a character after Kanto ended. Ash himself from Johto-Unova felt like the exact same character to me in his own right, mostly serving as the plot mover and maybe a foil to someone like Paul (who I actually do have some valid compliments about at times). Red is a character who is noticeably different and more developed by the G/S arc than he was when RB started.
Despite that, the series doesn't outright abandon characters either. In the anime, once Misty, May, Dawn, or Brock left the group, you can count the number of times the show really acknowledged them on 2 hands at most. Even after their particular arcs were over in RBG, Red and Green still made appearances as secondary characters for many of the subsequent arcs, even serving as mentor characters to the new characters at different times. They stay relevant even after their starring role has passed.
It also has a firm understanding of what it wants to structure itself as. Normal Pokemon has so many filler/between episodes between each Gym or Contest or (insert other character objective) that I feel like it's trying to choose between being an over arching narrative and slice-of-life show. The manga is focused on a continuous story, so while there are some filler/breath-taking chapters, almost every chapter of the story does advance the plot in some manner, at least relative to the game's progression. It's also less formulaic because they don't have to make the majority of the episodes "Team Rocket wants Pokemon, their device is electric proofed, new Pokemon stops machine, maybe Pikachu shocks them now and they blast off."
Last, one of my favorite things is that the manga knows just how loose to play with the rules of the game. If they do anything particularly odd, they make sure to reference something like a Pokedex entry to explain how it works, like Gengar's shadow abilities. They also acknowledge certain limitations, like Blastoise actually being able to run out of water if he shoots too long. While obviously not everything is imitable, in the games, there's a logic behind it rather than "Thunder Armor" or "Magmar makes the air so hot Electricity can't hurt it," things that for no reason only happen once or only one Pokemon can do despite not having a trait exclusively.