Either Gen, Double Blind or Feint Indication is a double agent.
- Who leaked that Twilight Sparkle was an alicorn. The only ones who knew were Spike, Celestia, Luna, Applejack, Rainbow Dash, Shining Armor, Intelligentsia, Double Blind and Feint Indication. The others have solid reason why they wouldn't betray Twilight, but we don't know as much about these three.
The twitches that Twilight keeps feeling in her spine and hooves are similar to Pinkie's Pinkie sense.
- As they happen shortly before Shining Armor's trial.
Earth Ponies and Pegasi can become alicorns if their wellsprings become sufficiently large.
- Its just not happened before.
- Its also unlikely because of the passive nature of earth ponies and pegasi magic. They tend to physically exhaust themselves before they drain their magic, so their wellsprings don't get much in the way of a magic workout. It might be possible if one were to slowly drain an earth pony's or pegasi's magic as a form of training. Drain, rest, drain, rest. Repeat as needed until the wellspring was sufficiently large enough.
Shining Armor will eventually ascend as well.
- Not necessarily during the course of the story, but he's got the potential. His wellspring is only a quarter of Twilight's, but he's still young, and its possible that he could potentially catch up by what would be considered old age for a unicorn.
- Alternately, he may already be an alicorn. We don't know how long Twilight has been an alicorn, only that she's discovered it fairly recently. We don't actually know what size her wellspring was when she crossed the threshold. For all we know it could've been the same size as Shining's is currently, only that he's given no indication that's he is one. For those who quibble that it's unlikely to have two alicorns coming from the same family, we only need to look to Celestia and Luna in that its happened before. Also, if there's a genetic factor involved, it's likely that it would run in families. Lastly, there one more factor to consider. Cadance has had a hard time conceiving a foal, and its been 15-16 years since they were married. We know that pegacorns have a hard time conceiving, but we also know female alicorns can not become pregnant. Is it possible that male alicorns become less fertile as they grow in power? Could that be a contributing factor?
One or more pre-Discordian alicorns are still alive.
- Celestia and Luna's library or Forbidden Magic was raided. This is deep stuff. Who could potentially make use of that stuff in a relatively short time frame but another alicorn? Add to that fact that some powerful illusion and mind altering magic has been tossed around in the series, and that points to the likely existence of another alicorn, possibly Lady Optika.
The Phantom is somehow connected to Lady Optika.
- She likely discovered a stash of Lady Optika's magical items in the past.
Starswirl is still alive and managed to somehow convey the contents of his spell to Mipaka.
- He found 'The After' not all it was cracked up to be and now wants to get out. If this effort with Mipaka doesn't work out, he'll try again.