Perhaps, Hylia is not the Goddess of Time, but the Goddess of Change. Time is forward motion. The seconds change, the minutes change, the hours, the days, the months, the years, etc. Time is part of change, so what if Hylia is the Goddess of that Change? And this makes Demise all the more Yang to her Yin, for Demise wanted to rule Hyrule for eternity. Time still flows, but the ruler does not change, nor his methods. Essentially, change is forever defeated and done away with. It makes sense to me, does anyone else see it that way?
