Well, a cool crossover might be the characters from Ben 10 being transported to the Naruto universe. Ben could team up with Naruto against common enemies. Ben could use his alien forms like Heatblast to deal with opponents who are strong against Naruto's ninjutsu. And Naruto could teach Ben about chakra control, which could in turn help Ben better control his alien powers when he transforms.
One interesting crossover could be Naruto characters getting access to the Omnitrix. Imagine Naruto being able to transform into different alien forms from Ben 10's Omniverse. It would completely change the way battles are fought in the Naruto universe.
In a more complex crossover, the political systems of both worlds could merge. The hidden villages in Naruto have their own hierarchies and rules, and the noble courts in Familiar of Zero also have a strict social order. If these were combined, there could be a lot of intrigue and power struggles as characters from both worlds navigate the new system.
One idea could be a crossover with the Powerpuff Girls. Ben could team up with the girls to fight a common enemy that is causing chaos in both their universes. Another could be a crossover with the Teen Titans. Ben's alien forms and the Titans' powers would make for some epic battles and cool team - up moments.
One interesting crossover could be Ben using his alien forms to help Batman fight Gotham's villains in a more unique way. For example, Heatblast could be used to deal with Mr. Freeze in a direct heat - based battle.
In some fanfictions, there might be a plot where the Avengers mistake Ben for a threat at first. But then they realize his good intentions when he helps them fight a common enemy. This adds an element of misunderstanding and then friendship, which is quite common and engaging in crossovers.
In some fanfictions, the technology in Ben 10's world might be combined with Stark's technology in the Avengers. Maybe Ben's Omnitrix could be enhanced by Stark's knowledge, creating a more powerful device that helps them in a battle against an alien invasion. This would involve a lot of scientific discussions and teamwork between Ben and the Avengers, especially Tony Stark.
In some fanfictions, Ash might get access to one of Ben's Omnitrix-like devices. This could lead to him being able to transform into Pokemon - human hybrids, creating a whole new set of adventures and challenges. He could use this new power to understand Pokemon in a different way and face stronger opponents.
One interesting crossover could be Ben using his alien forms to help the students at Hogwarts during a dark wizard attack. For example, his Heatblast form could be useful against ice spells. Another could be Harry Potter using magic to enhance Ben's Omnitrix. Maybe a spell that makes it transform faster or unlock new alien forms.
One interesting crossover could be Ben using his Omnitrix to transform into an alien that has the power to use the Force. For example, he could transform into a species that has telekinetic abilities similar to Jedi powers. Another could be the Ben 10 characters getting involved in the Galactic Civil War in the Star Wars universe. Maybe they help the Rebels fight against the Empire using their unique abilities.
One interesting crossover could be the characters from Highschool DxD using Ben's Omnitrix. Imagine Issei using the different alien forms to fight his battles in the DxD universe. It would add a whole new level of power and strategy.