How come in japanese anime, like a third of the episode is...?

It's called exposition, my friend, exposition. It exists simply to fill you in on what is already obviously going through the character's heads. I completely agree with you. If they just showed them thinking for a couple seconds rather than one to two thirds of the episode, and just let us fill in whatever they were thinking, anime would be a lot better off. Good question though. These kinds of things need to be confronted by the anime industry.