-Conclusion of episodes continue to prove Alsek's theory that I firmly believe in (I'll let him explain that one)
think quite a bit about the overall plot. More than anything, what got my attention was seeing Celestia defeated by the queen. It was... Really quite a shock. (shim will tell you, he saw my face when I watched it for the first time.) At first I was really mad because I felt like they used that as a cheap way of making the enemy seem really scary and powerful really fast at the cost of Celestia's character. But I got to thinking about it, and I realized how important it was to the story that Celestia was NOT all powerful and / or all knowing. Very, very little is known about the alicorns Luna and Celestia apart from that they overthrew Discord's reign of terror over equestria and put things in order using the elements of harmony. Supposedly they also defeated sombra, or, at least it's implied by a graphic of two alicorns with the sun behind the larger and the moon behind the younger.
They are both amazingly powerful, especially in tandem. However, there was a time before them, as we know from celestia's story about discord, and they are not invincible, as we know from the queen nearly overthrowing her. So while they've ruled for an age, it would only make sense that their time will come to an end someday in the distant future.
My theory is that twilight (in addition to her friends) were chosen to replace the two of them someday. You would have two ponies from each of the three tribes that each represented one of the elements of harmony ruling with twilight at the lead. I think this is why even though twilight has saved all of equestria 3 times total (4 now) celestia continues to train her and give her tests that are challenging even at her skill level. Celestia isn't preparing her like a normal student for living a life using magic for day-to-day mundane activities. She's training her to become a leader, and twilight doesn't even realize it yet.
Even the NAMES seem to imply this somewhat. Luna and celestia are representative of night and day, and twilight is somewhere in-between the two like middle ground.
We also have Celestia and Luna discussing twilight’s training together at the beginning of the premier like it's a matter of the utmost importance.
Luna: Are you sure you don't want me to go as well?
Celestia: Yes. Princess cadence and shining armor are already there. The others will be joining them soon.
Luna: The empire's magic is powerful, it can NOT fall again my sister.
Celestia: She WILL succeed at her task. And when she does, we'll know that she's that much closer to being ready.
As twilight and her friends ride off into the sunset on the train, Luna casts a spell that produces a thick book with twilight sparkle's cutie mark on the cover with some other symbols: