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.
Artemis could also be a great focus. She has a complex backstory in Young Justice, and in the Injustice world, she could use her skills as an archer and her street - smart attitude to navigate the chaos. Maybe she'd be part of a resistance group in the Injustice world, using her stealth and combat abilities to take on the regime. And her relationships with the other Young Justice characters could add depth to the story as she tries to bring them into the fight against Injustice.
Definitely Batman. He's a central figure in both universes, but in different ways. In Young Justice, he's a mentor, while in Injustice, he's fighting against a corrupted Superman. In a fanfiction, seeing how he'd interact with the Young Justice team in the Injustice world would be fascinating. He could be guiding them, but also learning from their more idealistic views. And his detective skills would be crucial in uncovering the secrets behind the Injustice regime and finding a way to overthrow it.