I'm calling it now. · 10:41pm Jan 18th, 2014
The mane six are going to realize the true nature of the virtues they all posses/ascend to true enlightenment, and the keys that open the box that came from the Tree of Harmony are going to be formed magically from their collective awakening, or something like that.
Or in less confusing language: those flashes of rainbow we keep seeing aren't just for dramatic effect, it's to signify when that particular pony realizes how to truly embody the element they represent/bear.
The thread from Coco and the badge from Spitfire are both "Keys". The rest of them will also be given by ponies to whom the Mane Six teach friendship lessons to.
I can see that.