I could never figure out what it was that supposedly attracted Hermione to Ron. He is of inferior intelligence, magical ability and sense. He is not especially kind or funny, and by the last book he is not even a particularly loyal friend. He has had minimal struggle in life, growing up in a secure, loving and happy home. And he is not particularly handsome or a sports star, which might have turned even Hermione's head. He is rarely nice to her, does not appreciate her and shares no interests with her, apart from being pals with Harry. I did not get it, and still don't.
I would have been happy for Hermione to end up with Neville, who is a person of courage, intelligence, fortitude and integrity, as well as a good wizard. But I personally saw her being too busy with her own goals to be bothered much with men in her early adulthood - especially her age mates, who would seem very immature. I think she would be far more likely to wait a decade or so and then marry someone like Kingsley Shacklebolt - someone mature, wise and accomplished enough to meet her on her level.
As for Harry and Ginny, if Rowling really wanted us to root for that match she should have given Ginny a personality of some sort. The only way that ever made sense was as a longing on Harry's part to really be a Weasley - to have a loving and close family. I agree with OP - Harry belonged with Luna. He was the only one who really saw Luna, appreciated her intellect, knowledge and openness to ideas, and didn't just dismiss her as a weirdo because of her eccentricity. As fellow outsiders Harry and Luna would have had a natural affinity, and she proved herself as brave and true as any of the heroes when the crunch came. Luna was underestimated by everyone. Except Harry. And Luna believed in Harry too. Plus she's pretty and sweet and original. So I was and remain Team Luna for Harry.
I was not too bothered by the toxic relationship aspect of Hermione and Ron, though I picked it up (I was an adult when the books came out) but I chalked it up to reflecting reality. Teenage girls do accept a ridiculous amount of immaturity and bad behavior from teenage boys. Teenage girls are too young to date grown men and the boys their age are idiots. (Or were in my day, anyway. I have three teenage sons now and I hope they have more sense.). Plus she will have grown up with people rolling their eyes at her passion and intelligence, to say nothing of her bushy hair. Anyone who has been a Hermione will remember how insecure they felt as a teen, and sympathise with her allowing herself to be treated badly by Ron. But I think she would have tired of him and dumped him long before marriage was on the cards.