Discord was the first to cross my mind. He was a brilliant villian. He almost destroyed the core of the elements of harmony - the friendship of their bearers and the qualities that made them earn them in the first place. If he only took a good care of Celestia it would be a finished deal.
Then, of course, Chrysalis, since she hasn't been completely defeated and/or reformed yet. She did have the best strategy, she used a perfect opportunity and fooled everyone - even Celestia herself, and Twilight, the only one who doubted her, gave up on her said doubts and apologised. Her defeat was out of pure luck of Shining and Cadence.
And also Starlight Glimmer. In a season 5 opening she was amazing - a clever brainwashing unicorn. But in the end of the same season she became overpowered (A unicorn stronger than an alicorn princess and an element of magic. Uh huh), redeemed with a cheesy speech and yeah...