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Man, imagine if Season 3 was like this, with Twilight dipping deeper and deeper into dark magic and needing to be purified with the Elements of Harmony, possibly with the help of an old student of Princess Celestia's...
Also, this could re-introduce King Sombra and reinforce the premise that he is very powerful and influential even when he's seemingly been dealt with by the good guys. Throw in Trixie getting mutated by the Alicorn Amulet and becoming an alicorn herself as another potential plot scenario for her and Twilight to have at it again as Alicorns next time (on friendlier terms of course).
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This would have actually been a better plot scenario. I mean as viewers of the show ought to know, Twilight does have a certain mastery of dark magic and I'm sure Trixie is unaware of this development. Near the end where Trixie swapped the amulet with the fake one, imagine if that didn't happen and Trixie wasn't fooled. Then Trixie would still have all that power and Twilight wouldn't have much to fall back on. Except her dark powers. She'd be against it at first I imagine, but seeing how Trixie is progressively losing her mind and how her friends and everyone else in Ponyville's livelihoods were at stake, she would feel like had no choice and resort to using it. She beats Trixie and Trixie vows to come back to beat Twilight next time. Now the bright side to this is that Trixie is defitinitely an established rival for Twilight and Twilight's dipping into dark magic influence her to become corrupted by its use in a future episode. The bad aide to this is that Trixie doesn't learn from her experience like she did in canon and further falls to the dark side. Some may like that idea, others may not. It's just a "what-if" scenario. I personally hope Trixie comes back as a friendlier pony, but remains the same personality wise and tries getting stronger to see if she could best Twilight in magic. Sort of like how Vegeta started out evil, but became more neutral by the end of Dragonball Z while still being Vegeta if that makes sense.