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Dem Ant,
Karl Kadaver: I have a pet fanon hypothesis that Celestia is secretly grooming Twilight for a position as some type of Special Agent for the Royal Government:

Even outside of Nightmare Moon and Discord, Ponyville has faced several threats to its existence over the course of the series (Dragon, Parasprite infestation, etc.). There is no obvious reason to believe that Ponyville is unique in this regard. In fact, its relative proximity to Canterlot suggests that crises of this nature probably arise less frequently here than elsewhere, if anything. So, we can tentatively state that these sorts of occurrences happen throughout Equestria with decent frequency. As an apparently benevolent and capable ruler (Tyrantlestia memes aside), Celestia would seek to curtail these crises. Although extremely powerful, and likely capable of handling any one of these occurrences on her own, Celestia is neither omnipotent nor omnipresent, so dealing with all crises at all times is clearly beyond her ability. Hence, it makes sense that she would maintain a network of information-gatherers and troubleshooters to protect Equestria and its citizens from major threats.
Twilight, without even knowing it, is being trained to be the leader of one such cell of operatives, or perhaps even the entire network. As shown in "The Cutie Mark Chronicles", Celestia noticed her magical aptitude and knew that she had the raw ability for such a position. Her time in Ponyville is serving as her preliminary training. The actual purpose of the letters is to serve as progress reports on her training, and she encourages Twilight to strengthen her bonds of friendship with the others in order to increase the power of the Elements of Harmony, knowing that these are a vital tool for ensuring the safety of the nation. This explains why, though Celestia could easily have done so, she hasn't personally handled any of the threats that have arisen throughout the series; she needed Twilight to handle them so she could advance in her training (Celestia was feigning ignorance about the parasprite infestation to keep Twilight from catching on to what she was doing).
Celestia allowed Discord to be released as something of a test, to see how far along Twilight had come (she knew that unlike Nightmare Moon, Discord is interested in chaos, not destruction, so she could be reasonably confident that none of her subjects would be seriously endangered by him as long as he was contained fairly quickly). Although Twilight performed admirably, she required some aid, however small, in the form of the letters. This signalled that she was not yet ready to operate independently. Hence, Celestia has continued Twilight's training regimen.
Although she was at first skeptical of the abilities of the other members of the Mane Six, Celestia has gradually become convinced that they would make excellent additions to her network themselves. This is why, near the beginning of Season 2, she instructed all of them to begin sending her Friendship Reports — she has expanded her training regimen to include them as well.
Derpy Hooves is a former member of Celestia's clandestine network who retired from a decorated career after sustaining a minor ocular injury in the line of duty. She now lives in semi-retirement in Ponyville to raise Dinky and Sparkler. However, she still takes on low-risk local missions for Celestia. Her current major assignment is to monitor the progress of the Mane Six and provide clandestine aid when needed. This is why we frequently see her in clever hiding places or blending into crowds near major scenes in which the Mane Six are involved. She has only had to directly contact Celestia in an emergency once — during "Lesson Zero", when Twilight's Want It-Need It spell spiraled out of control. After realizing that the Mayor had fallen under the influence of the spell and that she wouldn't be able to overpower her physically and bring her to her senses, she activated her Emergency Distress Call to signal Celestia. This is why Celestia appeared at exactly that moment. As it turned out, this was a convenient cover to expand her monitoring to the others through the use of Friendship Reports, so Celestia was not particularly concerned about it. Derpy's cover identity as a clumsy, absent-minded mailmare remains intact.
So, there you have it. The Mane Six are unknowingly being trained to be Secret Agents.
The hypothesis probably has several holes in it if you think about it long enough, but I like it all the same.
edited 21st Feb '12 7:26:40 AM by Hsere
"Someone who is nice to you, but rude to the waiter, is not a nice person." —Dave Barry