Well, a story where there is a mix - up of powers could be fascinating. What if the members of Team 7 got some of the Avengers' powers and vice versa? Naruto with the ability to fly like Iron Man or Hulk with the ability to use shadow clones. This would change the dynamics of both groups and create a whole new set of challenges and adventures for them.
Maybe the Avengers lose some crucial technology due to a heist, and they suspect it's the work of an international syndicate. The Mission Impossible team gets involved as they are experts in dealing with such groups. The two teams then have to combine their skills. Iron Man could work with the tech - savvy members of the Mission Impossible team to track down the technology, while Captain America and Ethan Hunt lead the strategic planning.
One great idea could be Ben using his Omnitrix to transform into an alien that has a power similar to one of the Avengers. For example, turning into an alien with super strength like the Hulk and having a friendly competition with him. Another idea is that the Avengers could mistake Ben for a threat at first because of his alien forms and then they realize he's actually on their side. They could then team up to fight a common enemy, like a powerful villain from the Ben 10 universe that has somehow made its way into the Avengers' world.
One idea could be that Nightwing is transported to the Avengers' universe through some sort of interdimensional rift. He then has to team up with the Avengers to fight a common enemy, like Thanos who has somehow acquired some of Batman's tech. Nightwing's acrobatic skills and detective abilities would be a great addition to the Avengers' power set.
One idea could be that Godzilla is drawn to the energy source of one of the Avengers' tech, like Stark's Arc Reactor. This causes chaos as Godzilla approaches the city where the Avengers are based. The Avengers initially see Godzilla as a threat and try to fight it. But then they realize that an even bigger alien force is using Godzilla's presence as a distraction. So, they have to find a way to communicate with Godzilla and work together to defeat the common enemy.
One idea could be that the Avengers are transported into the Street Fighter universe. They have to team up with Ryu and Ken to fight against a common enemy like M. Bison who has somehow gotten hold of some of Stark's technology. This would lead to interesting battles as the Avengers' powers mix with the martial arts skills of the Street Fighter characters.
Maybe Zelda herself could be transported to the Avengers universe. With her wisdom and magic, she could assist the Avengers in different ways. She could use her magic to heal the wounded Avengers or help Tony Stark understand some ancient technology that has similarities to her own world's tech. She could also provide strategic advice based on her experience dealing with Ganon in her own realm.
One idea could be that the Avengers are somehow transported to the wizarding world. They might be initially confused by the magic but then start to work with the Hogwarts students and teachers to fight a common enemy, like a dark wizard who has also harnessed some sort of Muggle - like technology to become even more powerful. For example, Voldemort could team up with Hydra remnants to create a super - weapon that threatens both the magical and non - magical worlds.
Imagine if Elena Gilbert was somehow connected to an Infinity Stone. This would draw the attention of Thanos, but also the Avengers. The Vampire Diaries characters would have to protect Elena while also dealing with the fact that the Avengers are now in their small town. There could be a lot of mistrust at first, but as they learn more about each other's motives and capabilities, they form an alliance to keep the Infinity Stone out of Thanos' hands.
One idea could be that Spider - Gwen somehow gets transported to the Avengers' universe. Maybe Doctor Strange's magic goes awry during an experiment. She could team up with Black Widow, sharing her acrobatic skills and they take on a group of villains together. It would be a cool dynamic as Gwen is more of a street - level hero while the Avengers often deal with bigger threats.
A great crossover idea is to put Star in a situation where she has to prove herself to the Avengers. Maybe she accidentally lands in the middle of an Avengers battle and they initially think she's a threat. But then she shows them her skills and they work together. Also, imagine Marco being friends with Spider - Man. They could exchange stories about their adventures and help each other out in their respective battles.