You could write a fanfiction about Ben going to an alternate universe where the Omnitrix works differently. In this universe, the aliens he transforms into have different powers and personalities. Or perhaps a story where Ben's identity as the wielder of the Omnitrix is exposed to the whole world, and he has to deal with the consequences, like becoming a target for every villain and also facing the fear and adoration of the general public.
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.
Well, you could write a 'ben 10 omniverse fanfiction' where Ben loses his Omnitrix and has to rely on his wits and the help of his friends to still fight the bad guys. Or perhaps a story where the Omnitrix starts evolving on its own and gives Ben new and unexpected powers. Also, a plot where an old enemy from the past returns with a new and more dangerous plan.
Another idea is to write a story about Ben's descendants in the future. How they use the Omnitrix or a new device based on the same technology. They might face new enemies and have different adventures.
One interesting idea could be how she would handle the different alien forms. Since Ben 10 has a variety of powerful alien forms, as a girl, she might approach using them in a more empathetic way. For example, when using the Four Arms form, instead of just brute strength, she could use it to protect the innocent more gently.
A cool fanfiction concept could be a crossover tournament. Ben 10 brings some of his alien allies, and the Equestria Girls bring their friends from Canterlot High. They compete in a series of challenges that test both strength and magic. Each team has to learn from the other's abilities and work together at times. This could lead to some interesting friendships and rivalries between the characters from the two different universes.
One idea could be a crossover where the Miraculous heroes and Ben 10 team up to fight a common enemy. Maybe an alien villain that is immune to the powers of the Miraculous but Ben's alien forms can counter. Another could be a situation where Ladybug's Lucky Charm combines with one of Ben's alien gadgets to create a super - weapon. And a third could be a story where Ben gets akumatized and the Miraculous heroes have to figure out how to save him without using brute force as his alien forms are very powerful.
Another idea could be a story where Spider - Man has to help Ben 10 when the villains from his world start causing trouble in New York. They would have to combine their different skills and knowledge to protect the city and stop the bad guys.
Another interesting plot could be that Myaax comes from a parallel dimension where she has different powers. In the fanfiction, she accidentally crosses over into Ben's dimension. Ben, being the hero he is, tries to help her get back home while also learning about her unique powers and how they could be useful against some of his usual foes. For example, her powers might be related to energy manipulation, which could be used to enhance the Omnitrix's functions.
A cool fanfiction could be Mal and Ben swapping powers for a day. This would lead to all sorts of comical and also challenging situations. For instance, Mal would have to deal with the responsibilities of being a king - like making important decisions in court - while having Ben's more 'goody - two - shoes' power. And Ben would be on the Isle of the Lost, trying to use Mal's magic in a place where it's not always welcome. Or a story where they go on a secret adventure away from Auradon, just the two of them, and discover a hidden land that has its own set of rules and magic, and they have to adapt quickly to survive.
For 'ben 10 x overs fanfiction', a great concept would be a crossover with the DC Universe. Picture Ben 10 meeting Superman. Ben could be in awe of Superman's powers, and they could team up to stop Lex Luthor who has somehow gotten his hands on some of Ben's Omnitrix technology. Or a crossover with the Justice League where Ben's unique abilities add an interesting dynamic to the team. He could transform into different aliens to complement the skills of each League member.