>>36881487They also gave additional details in the November 2009 issue of Nintendo DREAM.
copied from reddit which has a translation>Legendary duos represent opposite concepts, for example Groudon and Kyogre represent land and water, while Dialga and Palkia represent time and space. In the case of Ho-oh and Lugia, although they do not have a direct connection in the story, we imagine that they represent the sun and the moon, day and night, yin and yang (positive and negative), bottom of the sea and the sky, above and below.>Ho-oh and Lugia were born in the world of Pokemon Gold and Silver, for the new feature, time system, gave us day and night cycle. Thus, they represent the sun and the moon, day and night. 