Well, for example, Natsu's fire - dragon slayer magic could potentially interact with a heat - based alien form from the Omnitrix. Maybe when he's in that form, his fire magic becomes even more intense or has a different quality to it. He could use his dragon slayer skills to control the heat in a more precise way than the alien form normally allows.
Ben Tennyson is of course one of the most popular. Since he is the original wielder of the Omnitrix in the canon, he often takes center stage in fanfiction. Fans love to write about his new adventures and how he continues to grow and develop his skills with the Omnitrix.
In some Omnitrix fanfiction, there are crossovers with other universes. For instance, a story where the Omnitrix wielder ends up in the Star Wars universe. They have to use their alien forms to survive in this new and very different environment, facing off against Sith Lords and using their powers in creative ways to interact with the Force.
Well, Ben is obviously one of the main characters as the story is centered around him and the Omnitrix. Gwen might also be a main character as she often plays an important role in Ben's adventures, providing support or using her own magical abilities to help out. Grandpa Max could be another main character, offering his wisdom and experience to guide Ben through various situations.
What if the Omnitrix was actually a gift from a legendary Pokemon? In this fanfiction, Ash is chosen to receive it because of his pure heart and strong will. However, using it comes with a price. Every time he transforms, it drains his energy, and he has to find a way to replenish it. This could involve seeking out special items or places in the Pokemon world. His friends would have to help him manage this new challenge.
Obviously, Naruto would be one of the main characters since he has the Omnitrix. But we could also expect to see his usual friends like Sasuke and Sakura. They would be involved as Naruto uses his new powers. And perhaps some of the alien forms from the Omnitrix could be considered 'characters' in a way, as they would influence Naruto's actions and decisions.
Well, if Naruto has the Omnitrix in the fanfic, it would change the power dynamics a great deal. He could potentially access alien technology and powers that are far beyond what is normal in the Naruto world. This might lead to new alliances or enemies. Maybe the Hidden Villages would be both in awe and a bit afraid of his newfound powers, and he'd have to deal with the politics of that as well as any new threats that come his way.
Then there's Lyra. She's a female OC who is a brilliant scientist. She reverse - engineers some of the Omnitrix's functions and creates her own power - enhancing devices. She often teams up with other OCs and uses her intelligence along with the Omnitrix's powers to outwit their enemies.