Ok, here's what I think. I adore the books to no end but I don't really ship couples in HP (I ship Harry as a character and the story LOL) but I think that in the end, Ron and Hermione clearly belonged together: he's messy and sometimes immature (even if he came a long way) and Hermione's the opposite (even if she shows different sides of her)come on, it was clear they would end up together.I like the parts in book 4 and 6 when they're jealous of each other and there was this hidden chemistry waiting to explode.
About Harry...I was never a fan of Cho (but I was eager for the kiss to happen and how Harry would react) and when Ginny came along...it wasn't so sudden. JK gave hints like she always does and it's such a cute ship..a mature relationship for Harry and his ultimate true love..it feels natural as a ship, like they instantly fit, I don't know if you can understand that.
Harry and Hermione...I love their friendship, it's so beautifully built and for he first 3 books I thought they should end up together but after a while it's clear she's into Ron, Harry's not into her etc. I gotta say that, in the movies, Emma has an amazing chemistry with Daniel (especially in the 7th movie), more than she has with Ruper but that's just the movie, I take the book's authority first (LOL) and I seriously enjoy all their scenes together.