Superboy would be interesting as well. He's constantly trying to figure out his place in the world, and in a homefront fanfiction, he could be exploring his humanity further. He might get involved in community service activities to understand normal people better, which could lead to some really cool character development.
Miss Martian from Young Justice could be a great focus. Her powers of telepathy and shape - shifting make her a formidable opponent. Also, her experiences as a young hero trying to fit in and be accepted, especially when facing the more established Justice League, can lead to some really interesting character development and plot twists.
Superboy is often a popular choice. His complex origin story, being a clone of Superman, gives a lot of room for exploration in fanfiction. Writers can delve into his identity issues and how he fits in with both the Young Justice team and in relation to the Justice League.
Definitely Kid Flash. He has a connection to both Young Justice and The Flash. His relationship with The Flash could be explored further, like how he feels about being in the shadow of the more famous speedster while also being a key member of Young Justice. And his powers could be a great asset in the crossover, as he can keep up with The Flash in terms of speed to a certain extent.
Definitely Superboy. His complex origin story and his relationships with other characters like Miss Martian are always interesting to explore. Also, Beast Boy is quite popular as he brings a lot of humor and his own set of powers and emotional baggage.
Definitely Robin. He's a bridge between the two groups already. He has his own experience in Young Justice and is also an important part of the Bat Family. His character development could be really interesting as he tries to balance the two worlds.
Artemis would also be a great character to focus on. Her archery skills combined with Ghost Rider's hellfire could create some really cool combat scenes. Plus, her background and her own internal struggles could be contrasted with Ghost Rider's own tortured existence.
Flash is always an interesting character. His super - speed gives him a unique perspective and allows for some really cool action scenes. You can explore how he perceives time differently during battles.
One idea could be exploring the characters' lives during peacetime. For example, how they adjust to normal life after all the battles. Maybe they start going to school like normal teens and facing typical high school problems while still having their superhero identities in the background.
I think Superboy would be really interesting. In Young Justice, he's still finding his place and dealing with his Kryptonian powers. In the Injustice universe, he'd be faced with a very different version of Superman. He could be a bridge between the two worlds, trying to understand the darker side of power that the Injustice Superman has embraced while also holding onto his own ideals from Young Justice.
Definitely Superboy. His struggle with his identity could be interestingly explored in a gamer fanfiction context. He could be like a character in a game trying to unlock his true potential or find his 'true ending' so to speak.