Often, the clash of different powers and abilities is really interesting. For example, the superpowers of Young Justice characters against the magic of My Little Pony ponies.
The cultural exchange between the two universes can be a great plot point. Like how the heroes from Young Justice might view the peaceful society of Equestria, and how the ponies would react to the more complex and sometimes violent world of Young Justice. There could be ponies trying to introduce their ways of friendship and harmony to the Young Justice team, while the team might be trying to show the ponies how to defend against more serious threats. It makes for a really engaging story as they learn from each other.
The idea of a common enemy that forces the characters from both universes to work together is also very appealing. This enemy could be something that neither world has faced before, and they have to combine their unique skills and resources. For instance, a powerful dark magic being that is immune to the Young Justice's physical attacks but can be countered by the magic of the ponies, and vice versa. So, they must figure out a way to cooperate and defeat it.
One popular 'Young Justice My Little Pony crossover fanfic' is 'Equine Justice'. It combines the action - packed world of Young Justice with the colorful and magical world of My Little Pony in an interesting way.
One interesting plot point is the power dynamic. Naruto is extremely powerful in his own right, with his chakra and jutsu. When he enters the Young Justice world, it shakes up the existing power structure. For example, in some fics, his Rasengan is a completely new and unheard - of power for the Young Justice characters, and they have to figure out how to work with it. Another plot point is the clash of cultures. Naruto comes from a world of ninjas, with strict codes and traditions. In Young Justice, it's a different set of ethics and values. How they interact and influence each other is really engaging.
One idea could be that the Young Justice team has to prove themselves to the Justice League during a major alien invasion. The League initially doubts their abilities but as the battle progresses, they see the unique skills and teamwork of the young heroes.
Maybe there's a villain who has the ability to cross between the dimensions of Danny's world and the Young Justice world. Danny and the Young Justice team have to combine their efforts to stop this villain. Danny could teach them about dealing with supernatural threats, while they could show him how to work better in a team setting in a more traditional superhero sense.
Maybe there's a multiverse - related plot where the universes of Spider - Man and Young Justice start to merge. This causes chaos as characters from both worlds start to appear in the wrong places. The Young Justice team and Spider - Man have to work together to find a way to separate the universes again. They'd face challenges like dealing with different power levels and the cultural differences between their two groups.
One idea could be that the Young Justice team gets accidentally transported to an alternate dimension where the Justice League has turned evil. The Young Justice members then have to figure out how to reverse the situation while also evading capture from their once - heroes. Another could be a time - travel plot where the Young Justice team travels back in time and teams up with the early days of the Justice League to stop a threat that was thought to be long gone but has resurfaced in their own time. A third idea is that a powerful new villain emerges who can only be defeated by a combined effort of the Young Justice and Justice League, but first they have to overcome their differences in fighting styles and leadership.
One interesting plot could be that the Young Justice team gets accidentally transported to the Avengers' universe. They initially face misunderstandings as the Avengers are suspicious of these new, young heroes. But then they realize they have a common enemy. For example, a powerful villain is trying to take over both universes. So, they must combine their skills and resources to stop the villain. The Young Justice members' unique powers and the Avengers' experience would make for a great dynamic.
One idea could be that Spiderman gets transported to the Young Justice universe. He teams up with the team to stop a common enemy like Vandal Savage, who has some new high - tech weaponry. Spiderman's unique abilities like web - slinging and his spider - sense would add a new dynamic to the team's combat strategies.
A cool plot could be that a dimensional rift opens up and pulls some of the Young Justice characters into the Ben 10 universe. They then have to find a way to get back home. Along the way, they meet Ben and join forces with him. Ben shows them around his world, and they help him deal with some local threats. For instance, Aqualad could use his water - based powers in conjunction with Ben's Four Arms in a fight against a group of robotic enemies that are causing chaos in a city near Bellwood.
One idea could be to have Ben Tennyson end up in the Young Justice universe by accident. Maybe his Omnitrix malfunctions during a fight and transports him there. He could then team up with the Young Justice heroes to fight a common enemy like the Light or some new villain that's a threat to both universes.