She's a reincarnation of the Goddess Hylia. Aside from that explanation that we only just found out she does have strange abilities like being able to speak to Link in his dreams and such, not only that but her actions are that of someone very wise. Unless I've been playing totally different games up here in Canada.
I believe she was given the power of wisdom because the Goddesses wanted the people in power to be wise. They didn't want dumb people making bad decisions to rule their people. So they gave the Royals the power of Wisdom. Zelda may not always make the best decision but then again, she may not have a choice to begin with. She rules the people to the best of her ability.