Personally, I think that the box most likely contains new gems for the necklaces and crown. These new gems would "power up" the necklaces and crown, resulting in the birth of "2.0 Elements of Harmony".
Think about it. The box appeared from within a flower, which sprouted forth from the Tree of Harmony. And why do trees sprout flowers?
So they can bear their fruit.
And the Tree of Harmony's "fruit", in my opinion, would be these new gems.
(Since the old gems were part of the Tree of Harmony, when Celestia and Luna removed the old gems, they basically sterilized the tree. Giving the gems back to the tree finally allowed it to go into its flowering season.) But a tree's flowers can't bear their fruit unless they're pollinated, right? Well, that's where the keys come in.
The Mane Six will, in a sense, "pollinate" the flower by unlocking the box with the keys, thus allowing the Tree of Harmony to produce the new gems.
"But what will the '2.0 Elements' be called", you ask? Well, in my opinion, THAT has already been foreshadowed.
In Magical Mystery Cure, Celestia listed the "virtues" of the Elements of Harmony, although she referred to them in a "stronger and purer" sense.
These are the "virtues" that she listed: Integrity(Honesty), Charity(Generosity), Optimism(Laughter), Compassion(Kindness), Devotion(Loyalty), and Leadership(Magic).
These were the Mane Six's "1.0 Elements": *Applejack: Element of Honesty
*Rarity: Element of Generosity
*Pinkie Pie: Element of Laughter
*Fluttershy: Element of Kindness
*Rainbow Dash: Element of Loyalty
*Twilight Sparkle: Element of Magic
And, based on what Celestia said, these will be the Mane Six's "2.0 Elements": *Applejack: Element of Integrity
*Rarity: Element of Charity
*Pinkie Pie: Element of Optimism
*Fluttershy: Element of Compassion
*Rainbow Dash: Element of Devotion
*Twilight Sparkle: Element of Leadership
(C'mon, you gotta admit, my names for the "2.0 Elements" sound MUCH more awesome than those of the "1.0 Elements", particularly "Element of Leadership"(makes one think of the Matrix of Leadership from Transformers, though *XD*)!)
Moreover, as the "2.0 Elements" would essentially be the "fruit" of the Tree of Harmony(which would thus make them independent of the Tree), their power does not come from the Tree; rather, the Mane Six's friendship gives the "2.0 Elements" their power.
Oh, and we must not forget that Hasbro is consumer-driven. The "2.0 Elements" will undoubtedly look MUCH different than the "1.0 Elements"(chances are, in addition to the gem color, the shape of the necklaces and crown will change somewhat(looking more stylized and elegant, in my opinion)), which will require Hasbro to produce new toys as a result.
I don't think you're far off but I don't think they'd be new Elements. After all what would be the point? They gave the old Elements back to the Tree of Harmony so it can keep the Pillage Seeds at bay as well as the other dark things of the Everfree. Plus look at it this way, of the only times the Elements were ever really used by the Mane 6 were against Nightmare Moon and Discord. They were unnecessary for Chrysalis whom was defeated by Shining Armor and Cadence and then Sombra was defeated by the Crystal Heart. Clearly there are other artifacts that can stop the forces of evil besides the Elements of Harmony. What I do think you're onto is your pollination analogy. I personally think that there is a key representing each of the Elements of Harmony, however how and when they'll appear I cannot say. I honestly thought that they'd appear when each of the Mane 6 either teaches some other pony or rediscovers what their Element means. Rainbow Dash already basically re-learned loyalty with Daring Do as she was a loyal fan wanting to help but almost gave up even when Daring needed her. She also taught it to the Cutie Mark Crusaders when they were about to separate due to Scootaloo and Applebloom not getting along from their flag carrying routine. The key didn't appear so unless those weren't the moments I don't know what will bring about the keys. However as I said I still think each key is an Element and within the chest is a seed to a new Tree of Harmony or an equivalent. For all we know it could be something way different and far more spectacular than anything we can imagine at this point in time.
1: Although a seed for a new Tree of Harmony would allow the Mane Six to use the Elements again without worrying about draining strength from the Tree of Harmony(As the Elements came from the old tree, they would have no relation to the new tree, and as such the new tree could continue to keep the Everfree Forest in check without getting weakened by usage of the Elements), there's still problems regarding the growth of the Tree of Harmony. Specifically, we don't know how fast a Tree of Harmony grows, nor do we know if a Tree of Harmony is at full power the instant it sprouts.
(That is to say: A: The Tree of Harmony could have just been a sapling when Celestia and Luna were just fillies.
B: Even if the new Tree of Harmony is fully grown within a few seconds of its seed being planted, it does not yet have enough strength to keep the Everfree Forest at bay.)
2: (This one contains information in regards to MLP Generation 1)
I've heard some people say that the box could contain the Rainbow of Light from G1. Although it WOULD be nostalgic, I don't think that it would work out due to the fact that, unlike the Elements of Harmony, the Rainbow of Light is just a single item. And despite the fact that the G1 ponies all shared it to use it(eliminating the possibility of the Mane Six being divided over an argument of who gets to use it), the fact that it's a single item makes it much, MUCH easier to lose. And, moreover, the Rainbow of Light wasn't always reliable: it was (temporarily) overpowered by Tirek(villain of the G1 series premiere, and first ever villain in MLP history)'s "Rainbow of Darkness", and it failed to defeat the Smooze(villain of the G1 MLP movie) when the Smooze had only reached half of its full power(although that's mainly because the ONLY thing that can defeat the Smooze are the Flutterponies; in my honest opinion, this makes the Smooze the strongest enemy in all of MLP history). Plus, if the box's contents DO turn out to be the Rainbow of Light, then what will the Mane Six do with the necklaces and crown? (Of course, there's the possibility that the Rainbow of Light divides and forms new gems for the necklaces and crown.)
3: In regards to Shining Armor and Cadence as well as the Crystal Heart...they're all located in the Crystal Empire, which is a fair distance away from Ponyville. By the time Twilight and the Mane Six get to the Crystal Empire to seek help, they'll probably be too late to save Equestria.
4: The Mane Six didn't bring the Elements to the wedding because they didn't think they'd need them. After all, they were initially unaware of Chrysalis' presence. Moreover, the Changelings were initially referred to as an "unknown threat", which, in my opinion, this indicates that, unlike Nightmare Moon, Discord, and King Sombra, the Changelings are actually fairly recent. And due to how recent they are, Celestia was unsure if the Elements would work on them or not.
As for Sombra, Celestia and Luna were able to defeat Sombra without use of the Elements(thus, it's highly likely that they defeated Sombra before they removed the Elements from the Tree to use them on Discord). As such, Celestia was, again, unsure if the Elements would work on Sombra, although in this case it was because she knew that he could be defeated without them. Plus, she didn't expect that Sombra still had some strength left.
5: There have often been occasions were the term "Elements of Harmony" is used to refer to the Mane Six, not the gems.
In addition, there have been instances where the gems have reacted to the Mane Six.
Most notably, after Nightmare Moon shattered them way back in S1E2, they reconstructed themselves after Twilight told Nightmare Moon about how the Mane Six embody the Elements of Harmony.
Moreover, the extraordinary features that the Mane Six have regard their corresponding Elements.(Most notably Twilight's ability to copy magic spells just by watching them in action(examples being the barrier spell(which she learned from Shining Armor) and dark magic(which she learned from Celestia), Pinkie's gag-inducing physics-defying and fourth-wall-breaking antics, and Rainbow Dash being the ONLY pegasus pony capable of performing the Sonic Rainboom(and the first time she ever performed it in the show was to save Rarity(her friend) and some of the Wonderbolts(her idols) from falling to their deaths).)
What this could mean is that the power that allowed the Mane Six to defeat Nightmare Moon and Discord didn't come from the gems; it came from the Mane Six themselves.
(And before you ask why Celestia and Luna could use the gems around 1000 years before the Mane Six were even born, it's because Celestia and Luna possess the exact same power that the Mane Six do(that could explain why their Cutie Marks are also on the Tree of Harmony).)
All the gems did was just awaken their powers for them, and let the Tree of Harmony take the strain of using them for them(After the Mane Six used the Elements on Nightmare Moon, they briefly lost consciousness; obviously, using the Elements severely tired them out).
(But even though this WOULD be epic if it is true, it would render the box pointless.)
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