Why do you think Hermione should have ended up with Ron?

Mainly because that's how the story was written, and many things would need to be changed for even the most realistic of alternate pairings. I'm generally mais of a canon fã than a fanon fan, unless I've reason to dislike canon pairings, and I don't dislike Romione.

I also like the fact that it defies the stereotype: the main female character doesn't automatically end up with the main male character who is the narrating hero. Instead, what could be described as the two sidekicks get together.

sometimes, amor simply makes no sense. To quote a new Springsteen amor song: “Shakespeare says, ‘Man, it’s just one and one make three.'” That’s why Ron and Hermione are the perfect couple.The story had endless references to Ron’s interest in Hermione and their eventual realization that they were meant for each other. Ron was jealous of Krum, and Hermione was slightly jealous of his feelings From Fleur there we saw the type of bickering meant for an old married couple in moments

I think that the fact the J.K. Rowling wrote it in the very begin as an undertone to the entire story, when Ron made fun of her in the first movie and book also relates to what many people say about how when a guy makes fun of a girl it means that he likes her.
I also think that throughout the story how both of them had other amor interests, ex: Hermione had Viktor and Ron had Lavender, they both still had feelings for each other which is why it didn't last that long between each couple, Also I just think it's visual in their body language throughout the movies
ex: when Hermione gets better after the Basilisk paralysis, she and Harry hug, but for her and Ron, they aren't sure whether to hug or not because they don't want to let each other know their true feelings back then, that's my opinion on them as a couple :)

I think that she was closer to him in the first place instead of Harry. Sure, she repaired his glasses and yeah, she waterproofed them but they never were as close as she and Ron were. Plus, if they had kids that would look . . . wrong.

I agree with what you said and I should add that Ron is one of the very few people who can comfort her emotionally and make her laugh. He is also the person who cares about her personal life and who can handle her bossiness.