Well, they could have twin - like powers where they can combine their magic to create new spells. In the fight against the dark forces, this would be really useful. They could be the key to defeating Voldemort in a completely unexpected way. Their combined intelligence as twins could also lead to new discoveries in the field of magic at Hogwarts, like finding a way to make the Forbidden Forest safe.
A great plot could be that they discover they are twins later in their Hogwarts years. This revelation could cause a stir in the wizarding world. They might then start to explore their family history together, finding out secrets about their parents that were previously unknown. Maybe they find out that their parents had some special mission that they now need to continue as twins.
One plot idea could be their different personalities within the Gryffindor house. Percy is often seen as more rule - abiding and Hermione as more of a knowledge - seeker. Their twin bond could lead to them helping each other grow. For example, Percy could teach Hermione about the wizarding world's politics while she helps him see the value in more unorthodox ways of learning magic.
Another plot idea could be that the Riddle twins have a special connection to an ancient magic that Harry and Hermione need to understand in order to defeat Voldemort once and for all. The twins could hold the key to unlocking this magic, and throughout the fanfiction, they go on a journey with Harry and Hermione to discover how to use it.
Well, a plot could involve Hermione being influenced by a powerful dark magic item. This item warps her mind and makes her see Harry as a threat to the wizarding world. So, she betrays him by revealing his secrets to his enemies. Or perhaps she gets jealous of Harry's popularity and power and that leads to her betrayal in a moment of weakness.
Perhaps they form a secret club within Hogwarts where they plan elaborate pranks on the Slytherins. This could involve using their combined knowledge of magic and mischief to outwit their rivals in really creative ways. They might also end up uncovering some dark secrets about the Slytherin common room in the process.
One idea could be that they are adopted by a powerful but reclusive wizard. This wizard has his own motives for taking them in, like using their potential for a grand magical plan. Another plot could be that they are adopted into different families at first and then reunite later, realizing they have a special bond that goes beyond blood relations. Maybe they discover that their adoption was part of a prophecy protection mechanism, to keep them safe from the dark forces that are after them.
One idea could be that Harry and the Weasley twins team up to play a huge prank on Snape. They use a combination of Fred and George's magical inventions and Harry's invisibility cloak to get into Snape's office and rearrange everything in a really chaotic way.
One idea could be that Harry has to team up with the Patil twins for a special magic project at Hogwarts. They discover a hidden magical artifact in the library and have to figure out how to use it without getting caught by the teachers.
Perhaps they were separated at birth due to some family feud or difficult circumstances. In the fanfiction, as they start to realize they are twins, they face opposition from some of their friends or family members who are not happy about this newfound relationship. However, they persevere and use their musical talents to bring the two sides together.
One interesting plot idea could be how they initially react to the betrothal. Maybe Hermione is more accepting as she sees it as a way to strengthen the wizarding world, while Harry is more hesitant. Another idea is how they deal with Ron's reaction, since he has feelings for Hermione. They might have to work through their friendship with Ron while also coming to terms with their new relationship status.
A third plot could be that their presence in Ravenclaw changes the overall perception of the house. Usually seen as more cerebral and less action - oriented, Harry and Hermione bring a sense of adventure. They might convince their Ravenclaw housemates to join them in more dangerous quests, like exploring the Forbidden Forest for a rare ingredient for a potion that could help in the fight against the Dark Arts.