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 Subaru from 'Re:Zero'. His 'Return by Death' ability makes him a really unique character. In a crossover, seeing how he interacts with the super - powered heroes of 'Young Justice' would be fascinating. Also, Robin from 'Young Justice' could be interesting. His detective skills and leadership could contrast well with Subaru's more impulsive and desperate style of dealing with situations.
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.
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 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.
Definitely Superman and the Red Ranger. Superman is known for his incredible strength and moral compass, and the Red Ranger is often the leader of the Power Rangers. Their leadership styles could either clash or complement each other. Also, Batman and the Blue Ranger would be fascinating. Batman's detective skills and strategic planning could be contrasted with the Blue Ranger's more technical skills in handling the Ranger technology.
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.
Hermione Granger would also be an interesting character to focus on. She's extremely intelligent and curious. In a crossover, she would be the one trying to figure out how The Flash's powers work from a scientific and magical perspective. She might even try to find a way to combine magic and the Flash's speed for some greater good. Her inquisitive nature would make for some great interactions with The Flash and would add a lot of depth to the crossover story.
Batman would be really interesting. He's a master detective and strategist. He would be the one to study the Predator's behavior and try to find its weaknesses. His lack of superpowers but high intelligence would make for an interesting dynamic against the technologically advanced and physically powerful Predator.
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.
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.