It's a theory I've had mulling around in my head for a while. All the villains and problems the Mane 6 have experienced after they became the barer's of the Elements could Luna and Celestia be the cause of them? Now here me out before you write this off.

From our understanding of the universe, however small that understanding is, we know that Chaos and Order both need to be present for it to survive. The knocking together of opposites is how we can tell right from wrong, love from hate, life from death and so on. How can you know what light is if you've never known darkness?

So when Celestia and Luna sealed Discord, The aspect and god of Chaos away, thus sealing away the other half of their universe so to speak did they cause all the problems they got at a later date? The universe wanted to be whole, to have the the Yin to its yang back and as such kept trying to recreate the chaos that was Discords to control.

With Discord gone the universe kept creating different things to try and fill that gaping hole that was left behind by Discords imprisonment. Sombra, Tirek, Chrysalis, Trixie, Starlight and a host of others. When Discord had gathered enough power to finally breakfree and cause chaos once again The universe became whole but the damage had already been done hence why there are still other villains still popping up.

The balance of their universe was thrown out of wack and will take a lot of time to reset itself even with Discord back. So anyway that's my theory, what do you guys think? let me know in the comments.