I also want to make an AU out of this as well at some point. Twilight spent most of her life in a stallion's body, not thinking much of it. Although she never knew it, something felt off, missing. And after she was sent to Ponyville and met her friends, she began to realize what this feeling way. Not only did she discover friendship, but she began to discover her true self, and began to identify as trans. Although cautious as first, when she became more and more attached to her friends, she came out to them, and they have helped her discover her true self. Shortly after, the group helps Twilight gain the courage to tell Celestia, and eventually her parents. Although her parents where surprised, they learned to be supportive of Twilight's new identity. Celestia was immediately understanding of Twilight's feelings, and accepted her as is, and even making a promise to help her with a transition spell when the time was right.
Time passes, and Twilight's time has come for her next big chapter in life. After repairing Starswirl's spell and passing Celstia's final test, not only did Twilight transcend into an alicorn, but her body changed from a stallion, to a beautiful mare. The sensation of being in a body that truly reflected her true self, as wells as being granted the position of princess was overwhelming, yet exciting to her. She could finally express herself authentically, and she took her new role as princess very seriously. And it reassured her that her friends and mentor's would always support her and have her back no matter what.