I view Pokemon generally as intelligent, but still wild, animals. You look into the eyes of a wolf, for example, and you know that it doesn't want to hurt you, but that it also doesn't NOT want to hurt you. It simply doesn't care.
Legendary Pokemon are the same way. With the exception of roaming Legendaries, a legendary Pokemon will not initiate the fight(the exception to this is Groudon and Kyogre; even in story encounters like Dialga and Palkia you still walk to them first). I say that Rayquaza is purely neutral.