This is something that has occured to me after thinking about what happened in Flight to the Finish, particularly Rainbow Dash's handling of the Cutie Mark Crusaders.
Here's how Rainbow has evolved over the past four seasons. Listen to her berating the Cutie Mark Crusaders on the train. That isn't just the rah-rah Coach Rainbow talking anymore; her focus is on friendship and how that should be expressed particularly in the area of loyalty to one's friends. She's begun to personify the Element which she once bore. She has become Loyalty Itself.
Digibrony made this point in his review of Return of Harmony: In Season 1, the meta-plot was about Twilght learning about Friendship, reaching its logical conclusion in her being able to use the lessons to overcome Discord's manipulations. Thus, in Season 2 and 3, she was able to teach those lessons to the rest of the Six (hence them sending letters to Celestia instead). The last reference we see to that is in the otherwise-dire Apple Family Reunion, which I suspect was them fixing the silly and spiteful-sounding "I didn't learn anything at all! I was right all along!" from Season 2. Now, however, they've all learnt the lessons so well that, as we see with Rainbow here, they are able to teach these lessons to everypony else!
Celestia put it thus: "We are all your students now." I don't think she was just taking about Twilight either (although it's possible that she did not know this herself at that point).I'm wondering if this if the first hint of a meta-plot that's going to be repeated in several ways during this season - how the Six have become to personify the Elements so much that they may not need to wear the Elements themselves to call upon their magic.
We will see, but I suspect that Bats! (Applejack), Rarity Takes Manehatten (Rarity) and Pinkie Apple Pie (Pinkie Pie) might also have little hints to that end.
This feeds into my theory about the Box on the Tree of Harmony. I think that the keys will not be hidden anywhere but will be found in the Six's hearts (in metaphorical and possibly magical terms). Thus, the six of them together will be able to open the box but, ultimately, I suspect by that point, they will have already found the power they need to protect their world within themselves.