Why not Farore? Ceila, the spirit of courage from PH has the ability to stop time?
While I'll agree that Ciela being the Spirit of Courage and Time (Which is most definitely a deus ex machina) does suggest something greater, I think that the Goddess of Time is not only a separate deity, but the being that created the three Goddesses we know. Zelda's mention of the Goddess of Time, her presumed status as the Sage of Time, and Ciela's title could be a reference to a greater deity that influenced the main three.
First, let's refer to the timeline. Because there are three splits, I've seen the Adult timeline referred to as representing the Wisdom timeline because it is Zelda who sends Link back in time, and the Child timeline represents Courage because Link informs Zelda of Ganondorf's evil plans. I for one think that this is not how we should refer to the timelines, unless the names are what are given in the Hyrule Historia rather than just being fan designations. The Adult timeline is created because of Link's courage that finally allowed him to prevail against Ganon, but the Child timeline is created from Link sharing his knowledge of the future, and knowledge can be considered similar to Wisdom.
What's my point? Zelda refers to the Goddess of Time in a flashback that took place at the end of Ocarina of Time, which is on the Child timeline. In Phantom Hourglass, it is the Spirit of Courage that doubles as a reference to an aspect of Time. This means that a representative of each Triforce piece will reference the Goddess of Time, or at the power of time, on its own arc of the timeline. Granted, the Downfall timeline includes Oracle of Ages, in which the Harp of Ages is connected to Nayru, but then again, there's also the Rod of Seasons, which is connected to Din.