One key feature is the integration of different universes. For example, how well the rules and elements of the other crossover universe fit with High School DxD. If it's a smooth blend, it's usually a good sign.
One popular 'highschool dxd prototype crossover fanfiction' is 'The Hybrid Hero'. It combines the unique elements of the High School DxD universe with other interesting concepts. The story often has exciting battles and character developments.
One common theme is power. In both Prototype and Highschool DxD, power plays a crucial role. Fanfictions often explore how characters from one universe would adapt to the power levels in the other. For example, a character from Prototype might find the power of the devils in Highschool DxD either overwhelming or underwhelming.
One popular trope is the 'Fish out of Water' scenario. For example, a character from Prototype suddenly finding themselves in the Highschool DxD world full of devils, angels, and other supernatural beings. It creates a lot of comical and interesting situations as they try to adapt.
One idea could be to create an alternate universe where the main character has a different set of powers. For example, instead of the traditional Sacred Gear, they could have a power related to time manipulation. This would change the dynamics of battles and interactions with other characters.
One idea could be that the characters from Highschool DxD end up in the Hellsing universe. Maybe Issei and his friends are mistaken for new types of vampires due to their devil powers. They then have to team up with the Hellsing organization to clear their names and also fight against a common enemy that is threatening both the devil and human worlds in this combined universe.
A third idea is that there's a mix - up with the curses in both worlds. Ranma's curse of changing into a girl when splashed with cold water gets combined with some of the magic in Highschool DxD. This creates a whole new set of problems and adventures for him as he tries to figure out how to deal with this strange new situation while also trying to keep his identity a secret from the new characters he meets.
First, familiarize yourself with the original Highschool DxD series. Know the characters, their personalities, and the overall world - building. Then, come up with a unique concept or plot. It could be as simple as a new adventure for the main character or something more complex like a mystery within the school.
One great piece of fanfiction could be 'Prototype's Impact on Highschool DxD'. It explores how the abilities from Prototype might be integrated into the Highschool DxD universe. Another is 'Hybrid Worlds: Prototype - Highschool DxD' which combines the two worlds in a really interesting way, creating new storylines and character interactions.
Another approach could be a shared enemy. Suppose there is an entity that exists in both universes in a different form. Writers could create a story where the characters from Highschool DxD and Prototype have to team up to defeat this entity. This would require them to understand each other's powers and work together, leading to a lot of character development and exciting action scenes.