It's mostly because of the N64, and to a certain extent the GameCube. The library of the former was severely lacking in RPGs and other "reflective" experiences, AKA chill non-action games like VNs and classic adventure games, not only compared to the Saturn and the PSX, but the SNES as well. There was a certain cope among N64 fans, Nintendo's marketing teams and even Yamauchi himself that the N64 had a more "quality over quantity" library over its rivals. RPGs like Final Fantasy were for shuttered NEETs and gigachads preferred to play a very limited number high-fidelity action games like Mario 64 and Ocarina of Time over the entire trilogies of games that the PSX offered (it's certainly possible that this is how the marketing gimmick of the "AAA game" was born).
The smugness of the N64 fans and their disturbing adoration for a pair of games: SM64 and OoT, still has influence on what Nintendo fans see as "good" or bad games. This is the reason for why it was common during the DS/Wii and the 3DS/WiiU generation to hear that Nintendo had lost its touch, and now in the Switch era it's why some confidently claim that the only good games in the console are Super Mario Odyssey and Breath of the Wild, and that everything else is cheap crap.
Pokémon RPGs just have a very different appeal to what this millennial, forum dwelling audience considers "good". The series is not action-adventure and they have been exclusive to filthy pleb portables for most of its existence. The fact that Pokémon RPGs encourage multiplayer is a possible factor, which could also explain why Splatoon is also despised and overlooked in many Nintendo communities, despite being very polished 3D action games on the vein of Zelda or 3D Mario.
Furthermore, Game Freak is very far from the graphic powerhouse that Nintendo internal teams are. Nintendo first-party studios are some of the most important pioneers of 3D gaming, while GF released its first full 3D RPG just over 10 years ago. When GF released LGPE (a title in which the studio required the help of Niantic), Nintendo internal teams were already well-versed in HD development.
Now it's true that the N64 had its fair share of Pokémon content, but most of the praise is directed at Pokémon Snap which is, to the surprise of nobody, an action game! Pokémon Stadium was very well received back in the day, but the main attraction about those games was to see Charizard with the largest amount of polygons, not the gameplay.