They are so good because they are creative, original and new. The style of the stories are also fairy tale-like. The world building also has a lot to do with their successes.
Take world in spirited away for example. Another entirely different world for spirit inhabitants. You get to see what the spirits are like, what the lifestyles of the workers are like. How the world floods after heavy rain, the train, the stations and outside world to the bath house. The witches, magic, curse and spells.
World building plays massive part in stories. Its mostly why Harry Potter 1 was so great. The first time i saw diagon alley, i was blown away.
Another great thing is the way how they portray japanese culture. The animation, story and creativity in the films is really awesome. They give a cozy, dreamy and peaceful vibe, So sometimes when I'm depressed, lonely or even when its raining, I just go near the window and start watching one of their films. Even the Ambience in the films is good.