An old enemy of the Omnitrix's creator could be a great main antagonist. Maybe this enemy was locked away for centuries and now has escaped and blames the Omnitrix for his imprisonment. He would be extremely powerful and have knowledge of the Omnitrix's weaknesses that Ben doesn't even know yet.
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.
One idea could be that the Omnitrix malfunctions and gives Ben new, unexpected alien forms with powers he has to quickly learn to control. For example, an alien that can manipulate time in small bursts, which would create really cool scenarios where he has to fix things that went wrong in the past few seconds. Another idea is that a new villain is specifically targeting the Omnitrix and Ben has to protect it while also trying to figure out the villain's motives. Maybe this villain has a device that can nullify the Omnitrix's powers temporarily.
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.
One interesting storyline could be about Ben exploring new alien forms that were previously unknown in the official series. Maybe he discovers a form that has unique powers that he has to learn to control quickly to face a new and powerful enemy.
Another possible antagonist could be an alien scientist who was involved in the creation or discovery of the Necrofriggian babies. This scientist might have his own evil plans for the babies and sees Ben as an obstacle in his way. He could be using his advanced technology to try and capture the babies from Ben.
One idea could be that Ben discovers a new and powerful alien form in the Omnitrix that has abilities he's never seen before. He has to quickly learn to control it to defeat a new and dangerous villain.
One interesting concept could be exploring new alien forms that the Omnitrix can transform into. Maybe there are some hidden or rare aliens that Ben discovers in the fanfiction.
He could have a unique personality trait, like being extremely shy but when he transforms using the Omnitrix, he becomes super confident. For example, if he transforms into a big, strong alien, his normal timid self disappears and he becomes a fearless leader in battle.
You could also write a fanfiction where an OC is accidentally bonded with the Omnitrix in a way that it can't be removed. The OC then has to learn to live with it and use its powers for good, but they face challenges as they are not Ben. They might have to deal with people who are suspicious of them having the Omnitrix and also face enemies who are specifically after the device because of its new and unexpected host.
One possibility is that the story could explore how Gwen's personality changes when she has the Omnitrix. She might become more confident or more responsible. Also, there could be new villains who are attracted to the Omnitrix now that Gwen has it. She would then have to face these threats and protect the Omnitrix from falling into the wrong hands.