Alita is flawed, we've been over this in the Mary Sue topic (which she is not). Read the manga. The film does show this. She can be mischevious and a blood knight. Plus, she does get her ass kicked a couple of times, while gettting in an epic "Fuck your, mercy!" in one of them. Hell, she's been torn apart in the souce material several times. Hugo's case is obvious if you read the manga, but I've met several people who thought he would survive. And these are people who do watch movies, but never read the manga or seen the OVA. And she was an elite soldier (once again in the manga), so of course her memories of fighting are going to come back to her. Not that different from Jason Bourne. Sure he takes few more licks, but we're getting in to different genres at this point.
To be fair to Trunkage, the story does revolve more around her than it did in the manga. Especially motorball. In the manga, she was just one of the players. She played to challenge herself and learn something about herself. In the movie, the game is used as a ploy to kill her. The game revolves around her. There was so little time for motorball in Hugo's chapters. It should have been in a second movie. If they never made a second movie, then oh well. The logic of trying to do more awesome (be more significant and grand as Gordon_4 said earlier) is like trying to nonsensically squeeze the freeway chase from Reloaded into The Matrix. It has no place in the first movie.
Speaking of being exceptional, she doesn't even earn her stripes before running her mouth off at the bar. Her speech makes sense in the manga, because the Grewishka character (a combination of Zapan and Makaku) is a bounty who has killed hunter warriors. In the movie, he is after Ido and Alita. So what? Why should the other hunter warriors care? He doesn't even have a bounty. She looks like an idiot talking down to them, calling them cowards. It's no wonder they all conspire to kill her at the end, lol. Some hunter warriors use Ido’s business, but not all or probably even most. He can’t service a whole city for free. If the visitors there went to him, she would have mentioned it in her speech, called them out for not helping him after he helped them. She simply asks for their help against a "common" enemy (though I don’t remember the film ever establishing him as a common enemy), tells them he is protected by the system and then tells them he is now after Ido and her. There is a leap in logic there, like she forgot to explain how those things relate to everyone else. Besides, Ido only yells "No more free repairs” after everybody stops fighting, which makes the scene chronologically confusing and ineffective. She already made her speech and started hurting people before he yelled that. He yelled that after I had already made a mental note of the nonsense. He is an enemy to the others only indirectly. It would have been more effective to develop that character more beforehand, like in the book, and make him a bounty they have a reason to kill, like in the book.
There! That is adequate setup and sufficient dialogue! He has a big bounty and he has killed the hunters who have tried to take him, two things that are not true in the movie. The stakes are clear in the book and her stance is immediately understandable. It's a job, not just a personal problem. She calls them cowards for not having the spines to do their jobs and take this bounty. An actual bounty! If the scene wasn't going to work for their movie, then they should have built the story differently and possibly even dropped the scene.
Speaking further about being exceptional, the way the Berzerker body conforms to her looks too fantastic and fake in the movie. Regenerating instantly in the movie makes her too powerful.