OK so i have a theory or more a combination of theories that make sense to me and may explain a lot of history. So please bare with me on this one. Although not all of the theories are mine but together they seem to make sense.(ps Sorry about the bad Grammar)
So at the founding of Equestria, starswirl the bearded one of the most Powerful pony's (if not the most) who spent his entire life studding magic was suddenly surpassed in power by the two sisters through rite of birth, He grew resentment and looked into Crono (time) Magic to see if he ever gets as powerful as them only to see a much more powerful entity (Discord) be defeated by the two using magic elements of untold power.
Determined to be the most powerful he then went back in time to find the elements before the princesses just to find that there are between 12-15 elements plus a unique one so he took all but the six he seen Celestia and Luna use and the Unique one he couldn't understand (i'll get to that), as he didn't want Discord to win if he fails.
He then tried to use the elements he got to turn himself into an Alicorn, but not understanding friendship the spell went wrong and started mutating him. Before his fall into madness he gave the elements he possessed to the one person he trusted (his apprentice Clover the Clever) and told him to destroy them, But whatever he tried he was unable to.
However Clover the Clever fell in love with a beautiful (at the time)
Princess.but there people could never co-exist so he tried to alter the element of love and forge in into the crystal heart giving the people of what is now known as the Crystal Empire there new magic coat that made them almost immune to the draining effects of the changlings, While also making there love more powerful allowing both race's to co-exist and flourish together.
Chrysalis agreed to rule this new empire with Clover but only as partners not lovers so Clover decided to make a love potion to force Chrysalis to love and Marry him, but as Clover the Clever wasn't a good name for a king he decided to change it to somba.
But then Equestria was thrown into chaos by Discord (what Starswirl became) and as you know he was defeated by the Sisters. Witnessing the power they hold Somba decided to forge the rest of the elements he had into powerful items to defend his kingdom if need be and making sure to put a sort of safety feature on them such as the truth will break the Inspiration manifestation Books spell (that book rarity uses to summon stuff) or simply remove the Alicorn Amulet to stop its Corruption.
However when Somba was wearing the Alicorn Amulet he did not notice the corruption in him and the misery it was bringing to his kingdom, and as his hatred grew it overpowered his love for Chrysalis which intern broke the love spell on her.
Without the love spell Chrysalis seen that he had gone mad and in an attempt to save her kingdom she ordered and evacuation of her people while she headed to the sisters for help. as the changlings all had wings they flew over the wall somba had created but the rest where seen and enslaved for what somba can only see as betrayal.
As the two sisters fought somba he tried to cast a spell to bind himself to the crystal heart and as he was defeated and his body destroyed his essence was trying to re-manifest itself. seeing that he cant be stopped like that the two decided the only way to stop him was to banish the whole kingdom.
Chrysalis devastated by the loss of her kingdom and half of its inhabitants only to find that the two sisters decided that as the crystal pony's are the only ones who can resist the effect of the changlings, they exiled her and kind from Equestria leaving her wondering what she can do next.
After near 1000 years of starvation Chrysalis and her kind turn Malnourished and show signs of decay giving them there holey and disfigured look.
Now to fill in some gaps
1: The Unique Element
: It is the Element of Friendship (that magic key box thing) and as you can't have one person be a friendship it can't be wielded by one, but instead multiplies the power of the others by the strength of there friendship. thus making the rainbow powered Pony's
2: Why is Discord also Starswirl
:starswirl would have studied the elements to some degree and as he never understood friendship that much he never saw a purpose in the Unique Element until he (as Discord) befriended Fluttershy. which is why in the episode with tirek he points out that it might be important and urges them to unlock it. (maybe knowing that Tirek is going to get the Alicorn Magic and that it is the only way to beat him)
3: Why so many elements
:Well you see harmony in the perfect balance and we all know that having only good is not a balance which means to have harmony you must have Generosity and Greed, Love and Hatred, Honesty and Deception ext
4:Chrysalis saves the Crystal empire?
:this is an odd one but i never got the impression Chrysalis wanted to take over Equestria as she only attacked because she was discovered, I think she may be the one who found a way to bring back the crystal empire and planned on simply taking the throne and blending in to save her race from starvation as everyone in the crystal empire had amnesia they wouldn't notice a bunch of pony's (hidden changling) they never seen before.
5:Concept of time travel (irreverent)
:(i'll keep it short) now this one is more my theory of time. (in reality as well) i don't believe you can change time at all as if you go back in time then you where already there which could lead you going back in the first place and any action you do will lead to that moment aswel
:this can be seen in the show however. when the only reason twi goes back in time is because she sees herself and assumes there is something wrong which leads to her going back in time. and even if there was a catastrophe it would probably been because she stopped time and didn't know how to start it again leading to her going back in time to stop herself but when she went back she set the future in motion leading to her stopping time.(Sorry about that)
feel free to poke holes in my theory but i only know about the tv show and not even every episode. (this was before Season five)
i'm new to this does anyone know if this is the wright place to post theories?