You can start by giving her a distinct personality. If Twilight is studious and a bit reserved, make the sister more carefree and impulsive. Maybe she has a passion for art or music that sets her apart. Her appearance could also be different in a subtle way, like a different shade of mane or a unique cutie mark.
First, you can start with his appearance. He could look similar to Twilight but have some distinct features, like a different color in his mane or tail. In terms of personality, he might be more outgoing than Twilight. For example, he could be the type to easily make friends with everypony he meets. This would contrast with Twilight who can be a bit more reserved in new social situations.
One idea could be that the twin sister has a different magical ability. For example, while Twilight Sparkle is good at spells related to knowledge and friendship, her sister could be excellent at magic related to nature. This would create a contrast and also opportunities for them to learn from each other. Another plot could be that the twin sister gets into trouble in a different pony world and Twilight has to go rescue her, leading to all kinds of adventures in unknown places.
One idea could be that the twin brother has a different magical specialty. For example, while Twilight Sparkle is great at magic related to friendship and harmony, her brother could be more attuned to magic of the elements in a different way, like having the power to manipulate natural elements more directly. Maybe he could use his magic to help protect Ponyville from a new, different kind of threat that Twilight's magic isn't as effective against.
Flash Sentry could be a likely groom. He has shown an interest in Twilight in the past and they have had some interactions that could lead to a romantic relationship. Another option could be a completely new character, perhaps a powerful wizard or a prince from a far - off land who Twilight meets during one of her adventures and falls in love with.
A common theme is family bonds. These fanfics often explore the relationship between Twilight and her sister, whether it's a close, loving bond or a more complex, evolving one. Another theme can be self - discovery. Twilight or her sister may learn more about themselves through their interactions.
I really liked a fanfic where Bella's twin sister was a werewolf. It added a whole new layer to the story. Instead of being drawn to the Cullens like Bella, she was more involved with the werewolf pack. It explored how she tried to keep her identity a secret from Bella at first, which led to some really tense and exciting moments.
A common trope is the twin having a different supernatural ability. For example, she might be able to control the elements while Bella has her mind - shield. Another is the love triangle, but instead of Edward - Jacob - Bella, it's between different characters involving the twin. Often, the twin also has a secret she's keeping from Bella which drives the plot.
A likely candidate could be Discord. He is known for causing chaos and mischief. He might pretend to befriend Twilight Sparkle only to betray her at a crucial moment. Another possibility is Trixie. Trixie has been jealous of Twilight in the past and could betray her out of envy.
It could be a pony who is extremely extroverted if Twilight is introverted. Someone who loves chaos and spontaneity instead of Twilight's love for order and planning.