The manga did tone down the relevance of individual Pokémon (compared to the anime at least) and focused development mostly on the trainers. This would be an option to give trainers more Pokémon and also make the battles more game-like (switch if you're in a bad matchup). However, as the Pokémon are more interesting to the franchise than the trainers, it's not going to happen (and, in my opinion, a perfectly good way to handle it) - 5-6 Pokémon for Ash + a rival character, 3-4 for major supporting characters (Team Rocket counting as one character for this) and 1-2 for one-off trainers.
Anyways, there's a few things that I personally find disrespectful to the franchise:
1. Major roles in the game being extremely out of character - this is primarily noticeable in Gen 1, though there's a few modern examples (such as Colress).
Here's my opinions on the Gen 1 cast:
Professor Oak: Him being a poet is a nice addition to his character without being unreasonably out of place. Otherwise, it's also quite clever for him to manage Ash's boxed Pokémon.
Gary: Just as arrogant as in the games - he's one of the most popular characters for a reason. Still, I would have liked to see him use more Pokémon (Exeggutor, Gyarados and Rhydon come to mind)
Brock: Proof that Anime makers can't survive without shoehorning in a pervert. It's this cliché that keeps most people away from the medium. There's several animes who don't do that, but there's more than enough that do to convince the majority of people that anime is pervy.
Misty: There isn't really much that violates her in-game personality, but most of her character is just two traits: "Girl" and "Water-Type user"
Bill: Only thing worth mentioning is that they changed the DNA thing to a costume. Turning people into Pokémon might've been too big of a deal (still, there's Satochu). I guess they wanted to make something that's easier to animate or doesn't involve Ash handling a PC.
Lt. Surge: I think his condescending attitude is a little jarring, but not exactly unreasonable.
Erika: Way too exaggerated in her behavior - she's much more quiet in the game. Also, makes use of fart innuendos in battle - I think the writers forgot the move Petal Dance exists.
Koga: He's a ninja master. One of the few characters to be better than in the game - not only is his ninja presence more pronounced, he uses a much more fitting Pokémon (Venomoth instead of Weezing/Muk).
Sabrina: I don't know what made the editors turn the most peaceful character into a psychopath (forget the whip, Sabrina lets TR run free in Saffron and didn't do anything as you cleaned up). I guess they wanted to show off the Psychic-Type even more (even in Gen 1, it wasn't that good) and give a hint that is blatantly wrong (no, Gen 1 ghosts can't do squat against Psychics, but Chansey laughs at most of them).
Blaine: I like how they gave him a character trait based on his gym, but I think it might be a little overdone. It's a give and take, though, as his dialgoue isn't as hammy.
Giovanni: While is portrayal as a typical crime boss is alright, I don't like how much the writers bent over backwards to make sure Ash never encounters him. They could've easily made him get away after his plans were foiled, like all kid cartoons handle main villains.
Lorelei: Remember what Sabrina was like? It would have made perfect sense if Lorelei was the vicious, sadist freak who has no compassion for her opponents. Instead, she's just a typical study girl. Perfect chance to make a great introduction for the Elite 4 challenge, but if there's one thing the writers love, it's wasting potential.
Bruno: He barely even appears onscreen. All I remember is him showing up in battle in the first episode.
Agatha: Doesn't exist until Gen 2, where all of her canon traits are discarded and she's a random hermit instead. What.
Lance: Doesn't show up until Gen 2, either. Not even there does a get a significant role (his ties to Blackthorn City are written out, as is the fact he's the champion of the region).
Rambling over, next point:
2. Mishandling of the various types
I get it that you need to beat a Pokémon and not its type, but it's way too often that the Pokémon are better at countering things they're weak to than to fight things their own type (just look at Pikachu vs. Water Pokémon compared to his performance against Ground-Types). It goes to a point where you're stupid for actually trying to go for type weaknesses. Not to mention that a few type matchups are simply forgotten (Ghost is ineffective against Normal, but Noctowl is still vulnerable to Shadow Ball). There's also the fact that Psychic-Types are impervious to virtually anything and most moves of the type are interchangeable. At least they got the 'Dark is immune to Psychic' right.