When a Pokémon takes one of our available six slots in a game, it's not always an inclusion born out of love. Maybe we just need a specific type of Pokémon to deal with a threat. Maybe it's just a temporary inclusion, the best Pokémon we can find at that point in the game. Maybe they're just an HM slave.
Given that Pokémon games track our friendship level with each critter, it's not a stretch to say that Pokémon must feel the distance—and since they're smart, they must think about whether or not we actually love them.
Here's a heartbreaking comic by Steven Universe's Tiffany Ford, which explores the inner thoughts of a Pikachu that is having doubts about its trainer:
Man. That last panel. Makes me think about all the times I've put a Pokémon at a type disadvantage because I didn't really care. Aaaaa I'm sorry!