Generally, Omni-Man is stronger. He has superior physical abilities and a longer history of using his powers effectively. However, Invincible has shown potential to catch up over time.
Sure. Invincible's journey in the comics sees him continuously evolving and getting stronger. Eventually, he outpaces Omni-Man, but it's not an easy or straightforward path. There are many challenges and setbacks along the way.
Sasuke could be one. Given their complex relationship, there could be a situation where Sasuke's newfound power or different ideology leads him to fight and beat Naruto in a fan - made story.
Well, in a lot of these fanfictions, Stiles can get beat up due to his own recklessness. He might be so determined to solve a mystery or help his friends that he doesn't think about the consequences and ends up in a dangerous situation where he is outnumbered and beaten up. Also, there could be miscommunication. Maybe someone thinks he has done something wrong when he actually hasn't, and they take matters into their own hands and beat him up.
Maybe some new kids in the neighborhood who are trying to establish their dominance and pick on Lincoln as an easy target. They might not know much about him or his family, but just see him as someone they can bully.
It could be an antagonist character in the Septiplier fanfiction world. Maybe someone who has a grudge against Jack for some reason, like a rival in a game or a love interest situation gone sour.
In some fanfictions, Naruto might get beat up when facing a powerful new villain who has some unknown jutsu. This could be a villain created by the fanfic writer to test Naruto's limits.