Here's the context: Animal abductor Ash Ketchum is in rough shape after saving Pikachu from what could have been a fatal attack. They're on the ground together, Pikachu in his arms, when Ash takes the opportunity to ask Pikachu why he never wants to get inside a Pokéball.
Instead of pointing out the obvious discomforts of being shrunken down to the size of a Beanie Baby, and the added degradation of being strapped to a utility belt, Pikachu responds in an unsettling high-pitched voice with an uncomfortably tender reveal: "It's because I always want to be with you."
Needless to say, this is a really intense, private moment, and it's probably better that we pass over it in silence.
Generally, Pikachu is a yellow monster of few words, whose contribution is limited to, "Pika pi." This scene might be part of a dream/vision sequence of sorts, but there's only so much a fan can take, and even in a dream this is pushing acceptability.
The voice actor for Pikachu even weighed in on the controversy.