...is that Celestia has been grooming Twilight as her eventual replacement. This idea has been around in some form since the first season, with a few foundations holding it up.

1. We don't know if alicorns are born, made, or evolve to that status during life. (Or all three -- Cadence and Luna's reversion form suggest you can start young.) It may be possible for a sufficiently powerful or talented pony to become one. Twilight's already at the top of the charts for raw magical power. A little more pushing and...?

2. Celestia took a personal interest in her early. Word Of Faust is that Spike's hatching was not the standard entrance admission: Celestia suspected an Element-Bearer and swapped in the egg to see if she was right. She's been supervising the training ever since. To what purpose? Just to make sure she has a capable head of the local emergency response team? Something more?

3. Celestia is something over a thousand years old. If you look at the timeline, one millennium back was a crappy time for everypony -- Discord in charge to the south, Sombra taking over the Crystal Empire in the north, "And then there's something about a dragon", then the sisters got control of the majority of the continent, started to improve things -- and an outside force corrupted Luna... Discord said he'd forgotten how grim Celestia could be: she didn't exactly have a lot of reasons to be the light-hearted ruler of modern times.

The Fridge Horror page for the series notes that with the Grand Galloping Gala, she's been attending the same stuffy party for centuries. Her subjects worship her as a physical goddess and from all indications, that's the last thing she wants. What if she's just getting tired? Does she want to step down and be part of the herd again? But she'd need a replacement -- and either she feels Luna can't do the job on her own or there must be two for balance.

(Note Luna's reaction to Twilight's arrival in the first part of the episode. It's not necessarily all that friendly. Luna is trying to get everyone's respect back and her own sister not only doesn't seem to trust her with a mission, but may be training someone as her babysitter. In a word, ouch.)

But there are problems with having Twilight in charge of anything. If you want to imagine the future of the three Equestrian species under her rule, imagine a checklist under one hoof and a stopwatch in front of the other -- forever. Her OCD tends to run away with her and when she loses all control over it -- see Lesson Zero and stand way back. Sending her to Ponyville might have been an attempt to give her some balance by putting her in a social circle where she would have to moderate those compulsions. (Of course, she's arguably gotten worse... PTSD, anyone?) Give her a little on-the-job experience in dealing with the occasionally-insane citizens of the nation before you even remotely consider tossing her into the big seat and hope she learns a little calm from it. Even a little -- chaos (hi, Pinkie Pie!), as she's living proof that going too far the other way isn't exactly helpful.

Would you want Twilight in charge of a society? As she is right now, no. But then, from all indications, Celestia used to be pretty grim...

Another fan theory is that immortality for the Princesses was based on their connection to the Elements -- which is now broken and spread up among six.