The main character is Naruto as he is the one with the Omnitrix. But other characters from the Naruto universe are also important. Shikamaru, with his intelligence, could be involved in helping Naruto strategize with his new powers. Hinata might be there to support Naruto in a different way, perhaps being in awe of his new abilities. And then there are the various Akatsuki members. They would be interested in Naruto's new powers and might try to either steal the Omnitrix or find a way to counter it. So, while Naruto is at the center, the whole Naruto cast has a role to play in this fanfic.
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.
There could be original characters created specifically for the fanfiction. For example, a wizard who has some knowledge about the origin of the Omnitrix and tries to guide Harry. This character could be an old hermit - like wizard who has been studying interdimensional objects for years. Also, there might be a villain who is after the Omnitrix, someone who wants to use its power for evil purposes and constantly hunts Harry down.
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.
Obviously, Ben is a must - include character as he is the main user of the Omnitrix. Gwen can also be a great addition as she has her own powers and can provide support or be a source of conflict. Grandpa Max is another good character, with his experience and knowledge.
Naruto himself is often very popular. Since it's related to his world, fans like to see how he would interact with the Omnitrix and its powers. He could use it in his journey to become Hokage, or to protect his friends in new and exciting ways.
It's possible that Jiraiya could be a main character. He's Naruto's mentor, and in the context of Naruto having a curse seal, Jiraiya would be involved in helping Naruto either control it or find a way to get rid of it. So he would play an important role in the fanfic.
Most likely Naruto and Sasuke would be main characters as they are central in the original Naruto series and their stories can be easily explored in terms of having a 'dark side'.
In this fanfiction, Naruto might use the Omnitrix to gain various alien forms' powers. He could use those powers to fight stronger enemies in the Naruto universe, like the Akatsuki members. Maybe he would use the powers for stealth or super strength depending on the alien form.
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.
Well, obviously Ben Tennyson is a very popular character. He is the main character who wields the Omnitrix after all. His different alien forms like Four Arms or Heatblast are also quite prominent in the fanfiction world.