Desu I don't fully agree with Pikmin 2 being a dark game, but I do think it has a weirdly foreboding atmosphere and I can kind of see where you're coming from. The music in particular really underscores it, there are a lot more weird and eerie tracks compared to the first game (and a lot more tracks in general). Pikmin 1 feels like you're all alone on an alien planet, while the feeling I get playing Pikmin 2 is almost like the world doesn't want you to be there in spite of you now having some company. The caves in general are kind of gloomy too, with a few exceptions.