Author has written 4 stories for Digimon, Harry Potter, Card Captor Sakura, and Ranma.
I've got a few ideas that I think have merit the only problem is I don't think I can do them justice.
'Lilacs over Cherry Blossoms' what if Ino had befriended Hinata and not Sakura? We know that Sakura was almost as bad as Hinata before Ino saved her. What would Hinata be like if she had two blonds pushing her to change herself? Ino is the heiress of her own clan, and seemingly the best student after Sasuke so even Hiashi couldn't find much fault in a friendship between the two. Personally I think this small change would end up changing the story massively.
Another option that I've been thinking about for years now, is based off and idea from 'Escape with the Hokage's Hat' a wonderful story that, sadly, hasn't been updated in years. In it Naruto has been subjected to a number of extra seals that have all held back his growth, most where done willy-nilly and it could have gone horribly wrong and that got me thinking.
What if Hinata is the one under a seal matrix? One that started with a seal her father placed upon her, as is done to all hairs of the Hyuuga. A resister seal to help the heir gain both control over their chakra and increase the amount they have for better and longer use of the Juuken? The Kumo-nin who tries to takes Hinata, places a seal of his own upon the girl. One that is used on POW's and Nin-criminals. This seal was intended to take away not only her chakra but also her voice to not only insure she would never be a threat once she was safely in Kumo, but make it so she couldn't call for help during her capture.
After Hiashi kills the Kumo Ninja saving his daughter he then gives up his own life to keep his village safe from yet another war. Hiashi transfers Hizashi's seal to himself and dies either in the process or shortly thereafter to keep Kumo's end goal out of their hands, and to free his brother from his prison. However, Hizashi tells no one of this switch and instead takes over his elder brother's life. He starts favoring his 'nephew' and 'younger' daughter over the 'weaker' Hinata.
Other members of the clan start adding seals to the matrix to, "Help" Hanabi to take her "rightful" place in the clan. The matrix comes to light after a spar with Neji disrupts it and "Hiashi" takes his daughter, who he now as a better relationship with, to the hospital and Tusnade gets a look for the first time ever.
Once the seals are removed Tsunde gets to thinking, the first seal, the one that started it all was something that Hiashi should have known about...
Its complex and once again something I don't think I can do justice to if I write it. Though, as you can see, that hasn't stopped me from starting. I'm setting it after the Chuunin exam once Hinata and 'Hiashi's' relationship is shown to be better, however right after Neji beats her down in the exam could be vary interesting. Even if it would mean she is either bed ridden until Tsunade returns, or Jiraiya is the one who takes a look first.
Oddly, once Hinata is freed of the seals I could see her acting much more like the RTN Hinata. The POW seal didn't work properly, as it was in conflict with the older seal, and the Kumo-nin placed it in a hurriedly and sucked at seals, but it did make her far more shy then she would have been. Once freed of that...
One last idea is much newer then the others. I've read quite a few Naruto with the Rinnegan stories over the years with new ones showing up every once in a while. In most, so long as its a Naru/Hina, Hinata dies, quite often in wave, and it brought back as one of the first things, if not THE first thing that Naruto uses his new eyes for.
With The Last out now and showing that the Byakugan does, in fact, have a 2nd level to its power and that Hinata is the chosen of her own bloodline, the she should come back with the Tenseigan. After all, any relationship needs to be between equals. And a kyuubi powered Rinnegan using Naruto is so far out of Hinata's level that she needs something to bring her closer to that. The effects of the Tenseigan, as seen in The Last, would go a long way in letting her reach that equal level, at lest against one or the other (Naruto using both the Kyuubi's power AND the Rinnegan isn't something she could touch without her own demon, sadly).
I've always liked time travel fics, and I've had an idea for one of my own, one that I'm honestly surprised I've never seen someone else think of. Years down the road an old Hinata dies in her bed surrounded by friends and family, only to wake up face to face to an extremely young Sakura who is looking quite shocked and a crater where Kohona should be.
You see, what if Hinata HAD died to Pain's attack, only Sakura brought her back before he used his last jutsu to revive all that he had killed? Even if she was only dead for a moment before Sakura brought her back his jutsu would still have 'effected' her would it not? As such she has lived with a single 'save file' and is now back to that single moment in time has to relive the horror of war.
But this time she has the knowledge of about 100 years of living and the power of Hamura, she could end this war on her own if necessary right? Save Neji from his fate. But then its been 100 years, the events leading to the war are old and faded...