Per this thread, I started reading the books on Friday and am now half way through Azkaban.
One thing I've noticed is how blatantly Hermione/Ron is pushed on the reader. I'd never call my self a shipper, but I do remember how I seemed to think way-back-when, that's how things were headed.
The first thing that stands how is how, post troll scene, Ron is ALWAYS the first to react/get mad at Hermione's peril (usually induced by Malfoy). And half the time he is the only one who does so as Harry doesn't react at all--all.
About the troll scene, it should be pointed out that it was Ron, after all, who actually vanquished the troll and thus saved Hermione. Really, Harry was kind of useless.
Then there is the obvious "ball and chain" type relationship JKR tried to set up between Ron and Hermione. It's just another example of an old archetype she used to get her point across.
Also, while not otherwise very important, it should still be noted that the first person Hermione ever speaks to is Ron, not Harry.
Another thing I've noticed is, when ever Ron actually seems to do something good or positive it s the direct result of Hermione's influence and not Harry's. In fact, Harry seems to pretty much just have a negative effect on him.
About Harry and Ginny, it's never been a big deal. To me, it's seems like JKR catering to the bigger number of fans.
However, she did write how she "loves" Riddle in the diary, and the main point of CoS is how Harry and Riddle are the same.
And Ginny is the first (and really, only) person Harry rescues in the old, "Hero saves girl, hero gets girl" sense. She was the damsel in distress; Hermione never really was.
It's also hinted at, especially through the later books, that Ginny is Harry's magical equal--one can infer this is because she is the seventh child and there is a lot of reference to the importance of the number seven throughout the books. She is also his equal (if not better) at Quidditch. Apparently bit that was left-out of the Epilogue has her going on to play professionally.
As far as Harry's sudden fawning of Ginny, I actually think that's fairly normal. I also think for him to have that realization of Hermione is not normal.
It's pretty rare for a guy to suddenly go gaga over a girl he's spent his life having and intimate, but strictly platonic "sisterly" relationship with. After a while the portrait of that person becomes so etched into the mind's eye in such a certain way that it's hard to erase it and start over.
On the other hand, to have someone you're friendly with but don't no so well that you aren't completely aware of all her thoughts, idiosyncrasies, etc and experience something that makes you see her in new light, really isn't all that unheard of. Now, for the story's sake, it might not have been the best way to go, but it certainly isn't unprecedented.