I can understand why there are so many people out there who likes Hinata as much as they do. For in a way I am one of them. During part I we had 2 girls who were possible matches for our dear dense Naruto. On one hand we had Hinata who "trully" loved him, even in secret and on the other we had Sakura, who Naruto was deeply infatuated with.
At the point of the Chuunin arc, Hinata had appeared as a shy, yet sensitive girl who trully cared for Naruto despite all his flaws, and given the chance, was ready to step in and support him in any way he would need. We must also remember that Naruto (at that point specially) had never known love, neither from mother or father, friends, relatives or anything (Obs. Considering the sacrifice made by both Kushina and Minato, it still stuns me that both Sandaime and Jiraya and Kakashi allowed Naruto to be all alone for his entire childhood). So Hinata presented herself as someone ready to love Naruto, and to make him feel accepted. This situation was touching to those who liked the baka.
On the side, we had Sakura, pretty, popular and totally shallow. She just didn't give a damn about Naruto's feeling, and only recently had began to change her opinion about him. Her feelings for Sasuke were totally biased and unfounded, for she didn't know him at all, apart of the fact that he was a "Uchiha" and "popular". In truth, this is the worst kind of person there is in the world.
At this point is it perfectly understandable why so many people would prefer Hinata over Sakura. I did as well. But as events unfolded, Sakura began to change and realize who naruto really was, and also to draw strenght from his character. For Hinata, she was left in the sidelines. Hinata's backstory had a thousand possibilities, including the entire "clan affair", but that was never developed by Kishi.
As time went by, Sakura changed from a spolied shallow brat to a strong and sensitive girl, really supporting naruto and standing by his sides. Even more, she became his best friend, despite all his shortcomings. Hinata remained the same. So far the only thing Hinata did in part 2 was to jump in front of pain and say "I love you". Some may argue it was a selfish act, other a selfless one. I 'd rather go with the latter,but still it doesn't change the lack of attitude of her part. She had had plenty of time to mature, as most of the characters did, yet, she remained the same.
Regarding the Hinata fanbase/ Sakura bashing, there is one point I didn't see mentioned on this topic. Most ppl say it's because she is shy, motherly ( I think sakura is more motherly, specially considering both Kushina and Shimamaru's mother - his father fears her), tender, submissive, etc, or just because she has 2 torpedos in front of her. However in analogy we could call the "dansel in distress" syndrome.
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The subject of the damsel in distress, or persecuted maiden, is a classic theme in world literature, art, and film. She is usually a beautiful young woman placed in a dire predicament by a villain or a monster and who requires a hero to dash to her rescue. She has become a stock character of fiction, particularly of melodrama;
For some reason, some men feel atracted to woman in danger, not that she ever was in real danger, but she had the whole "need to be rescued" aura around her.
Sakura was the strong character, the one who would impose herself and do what needs to be done - or so she tried. However many men have difficults accepting a strong woman by their side, they feel unmanly, and would rather go for a more submisse girl (Hinata in this case). It seems we (men) have deep issues accepting help from women.
Now, as the story stands Sakura made a real effort to get closer to Naruto, even if not a romantic way, at least in a caring and tender manner. I recently read a manifesto talking about Sakura's development and I find myself agreeing with most of it. The character she is now has nothing to do with the one she was in the beggining of part I.
Besides all this, we still have the entire past generation/new generation theme to discuss. It is hardly a coincidence that Jiraya became Naruto's sensei (as he was Minato's) , as Tsunade became Sakura's and Orochimaru Sasuke's. At this point history (in the manga) is repeating itself all over again, but I believe it will turn out differently if only to show the new generation has learned something from the old one.
It is hardly a shock to realize that Naruto is a Jirays 2.0 (not as perverted though), and the same goes for the others. Yet Sakura witnessed how distressed Tsunade became after knowing of Jirays death, and i believe that Sakura perceived how much her sensei loved the Ero-sennin, even if she had never acknowledged the fact herself. In a way, this opened the possibility to allow Sakura to actually admit the possibility of loving Naruto without knowing it, also how lonely her life will be if she insists in the same mistakes of Tsunade.
Another comparison we can make without fear of wronging ourselves is between Naruto and Minato. Since part I many characters talk about how much Naruto reminds them of the Yondaime, and not only in appearance, but also on attitude. I believe there is an interesting theory that could apply here about why Naruto is so dense - every other child, even Sasuke, had parental support as they were growing up, and those in shiobi families were trained and taught since the youngest age. Naruto never had anyone to rely on, and was always left to his own design, never had anyone to impress, or to guide him, therefore, never saw the need to apply himself in the studies; all he cared was to become strong (not knowing the relation between strenght and knowledge)
Back to the comparison, we have Kushinga, who had a very strong character, attitude, not to mention her strenght and abilities. This somehow reminds me of Sakura (lol), who shows similar traits. Also Kushina's first impression of Minato were far from civil, such as were Sakura's first impression of Naruto.
I will not bet anything, since it all depends on the will of Kishi, however, it is my belief that he is rewriting the old generation history anew with naruto and the others. Maybe he wants to show how the new generation has surpassed the old one, as is commonly said that Naruto has surpassed both Jirays and Minato. If this turns to be true, it is clear that Naruto and Sakura will end up together.
My only fear regarding this pairing is that Sakura just doesn't "settle" for Naruto due to the lack of Sasuke. That would be terribly wrong, and an undeserving end for the history.
For Hinata, I believe that Kishi has taken a different turn. The scene where she is fighting alongside Neji raised some suspitions in my mind, and I believe somehow they will end up together (cousins can properly marry, right?). For one side she is the Hime, and heir of the Hyuga family, for the other, Neji is the most gifted Hyaga in history (not sure, but one of the most at least). It would also be a way to break the main family, support family curse, by marrying the heir to the main family with one who was "branded". Can't say it will happen, but it would surely make a nice development for the situation.
Again, just my 2 cents...