I may be overthinking on this, but I think when one looks at this in perspective. We may have lost the Elements of Laughter, Kindness and Loyalty, and a very special dragon :(
However, looking at the survivors I see how balance in Equestria could be achieve with the many losses that occurred during the game
Elements of Harmony
- Twilight Sparkle - Magic
- Applejack - Honesty
- Rarity - Generosity
Possibilities and Why
- Derpy AKA Muffins (Laughter) - She is the most comedic one of the group. Her being scatterbrained and accident prone make up for the comedy but she is also diligent and does her best when given a task. Pinkie has a respectable successor right here.
- Sunset Shimmer (Kindness) - She may have had a rough start, but a pony like Fluttershy would've looked past all her sins if she was repentant. Sunset also displayed an ability to emphasize with creature (Human or Pony) when they walk down the same path she did (Sci-Twi). Her newfound kindness is a strong asset to her character.
- Scootaloo (Loyalty) - She looked up to Rainbow Dash, and she always knew that when her friends needed her despite whatever fears she may have had, (Flight to the Finish and Sleepless in Ponyville) Scootaloo would never let her friends down and always came through. It's something her idol would've done.
Raising the Sun and Moon
Twilight being the only alicorn here has a potential chance to be to one to raise the Sun and the Moon. It would take a lot of training, learning about magic is something Twilight would jump at the gun at.
Crusader's Possible Destiny
Scootaloo, out of respect for her late friends, would do all she could to see that ponies understood what their cutie Marks meant besides helping them get it.
The Crystal Empire
Once again, Twilight would have to do more work and oversee the Empire, OR, she would take the time to find a worthy successor to Cadance.
I think balance could be achieved this way if something like PAWG really happened. As Jurassic Park put it: Life will find a way.
But what do you think? Did I miss any thing? Do you have any other ideas?
Let me know in the comments.