But yeah, I HAVE been thinking about ways to do this better. Off the top of my head...
Just overall, make Fuuka's character more consistent. She seems brash and impulsive and quick to fight in the first bit of the first episode and then that trait very rarely shows up again. She's perfectly calm when getting fired and thinking she's going to have to go back to the orphanage! WHY. So, give her more of a developed character, give her flaws that cause problems for her, and give her some hangups! Come on, Rinne's a psychological issue treasure chest, Fuuka's gotta have some issues over that percieved betrayal and just her time as an unadopted kid. Let her resent the other girls for their casual easy paths through life! Let her be suspicious and untrusting towards Nove taking her in!
Also overall, fix the details to make this more Nanoha. Make the cars not obviously Earth models, reference details of Mid culture that don't seem lifted from Earth, freaking worldbuild. Additionally, for the love of god, add more magical combat. Have Scuderia talk. Anything.
Then, for the actual plot... first, straighten out what Rinne's issues are and what Fuuka thinks they are early. Does Rinne actually hate weaker people? Then work that in with her later characterization rather than having her be readable as just really awful at socialization. Is Fuuka meant to be reading her wrong? Then have that become clearer and actually have her REALIZE that.
When we get to episode... whatever it was, with Fuuka learning how to fight properly. When her second fight with Vivio comes, don't have her win with the Hegemon fist. Instead, she's integrated everyone's attacks and techniques together, or started working on that, and manages to surprise Vivio. She also uses more obviously magical attacks, rather than just punching. However, have Einhart visibly use sky-splitting knuckle in Fuuka's view. Then, when the invitation to the tournament and subsequent fight happens, Fuuka still uses the hegemon attack, but it's not perfected. Einhart is surprised to see that, after just seeing her practice it, Fuuka has managed to make a somewhat functional copy. They decide to focus on honing Fuuka's skill for integrating everyone's techniques, and have her learn them properly instead of copying them by eyesight.
Then, when this final battle happens, cut out everything about the god's fist. Instead, make it clear that, sure, Fuuka's not got Rinne's overwhelming natural talent and durability, but her techniques learned by the support from all her friends are the perfect counter for Rinne (who, from the Vivio fight, seems to have a major issue with adapting to sudden fighting style changes.) That way, Jill's ideal is disproved, and we get the clear thing of Fuuka getting strong through her friends.
Blah blah fight with WAY more magical attacks than are had in the current one, get creative, it's your finale fight. Rinne switches to bombardment attacks to gain distance, Fuuka throws some back with Hegemon techniques. They fight, they work out their issues, the flashbacks are worked in more elegantly somehow (maybe seed them throughout the series instead of having them ALL now? just a thought) and in the end they KO each other. Maybe Fuuka manages to stay conscious just a little longer and they still hug in the puddles, but in the end it's a draw.
Then... well I have no idea what the finale holds. But Rinne and Fuuka promise to settle their fight sometime. Many, many times.
....this is all come up with off the top of my head, pretty much. And I haven't rewatched any episodes since my first viewing. But still.