1. They have mutual respect for each other.
Professor Lupin says Hermione is the “smartest witch of her age” he’d ever met, and throughout the books she proves this to be true countless times. More importantly than Hermione’s genius is that she alone of the Golden Trio really teaches Harry any useful magic.
She coaches Harry on how to perform the Summoning charm before the Second Triwizard Task, she realizes how to use the Time-Turner to save Sirius (RIP), and she is literally the only reason Harry survives past book five. In his defense, Ron helps Harry every chance he can get (when they aren’t fighting), but never really imparts great wisdom to Harry.
On the other hand, Harry teaches Hermione about friendship through acts of loyalty and bravery, things she may not have picked up from Ron.
2. They don’t get into petty fights.
With all due respect to the many fantastic romantic comedies out there, two people who argue CONSTANTLY about the tiniest of details usually don’t stay in relationships for very long (Blue Valentine, anyone?).
Ron and Hermione literally fight throughout the entire series and Harry even gets mad at them for always being at each other’s throats. When Harry and Hermione get into a fight when she rats out his broomstick’s origins to McGonagall, Harry makes up with her because he knows her heart was in the right place.
Their friendship is always more important to them than being right, and this sets their relationship apart from Ron and Hermione’s relationship.
3. Other characters believe they are together.
In the fourth book, Rita Skeeter writes that Harry and Hermione are dating, leaving Ron angry and jealous at them both — while neither Harry nor Hermione get that mad at all.
In the fifth book, Cho Chang makes the snide comment, “Oh yes, I forgot — of course, if it was darling Hermione’s idea…” when Harry says Hermione would be joining their tea party. It doesn’t even cross Cho’s mind that Hermione and RON could very well be dating, because it really is not as believable as Harry and Hermione.
4. Hermione chooses Harry over Ron.
When Ron succumbs to the pressures of the Horcrux and tells Harry he’s leaving because he’s lost faith in their mission, Hermione refuses to go with him.
Why? Because Hermione absolutely trusts Harry and his plan, regardless of how it was currently unfolding. She didn’t need to see instant results to know it was the right thing to do. Although Ron regrets his decision almost immediately, Hermione never has to. She chose Harry because she believed in him more than she cared for Ron.
5. They understand each other.
In Harry Potter and the Order of the Phoenix, Hermione makes the calculated decision to bring Umbridge deep into the Forbidden Forest in hopes that she would attract some dangerous magical creatures, and she does so by promising to reveal all the DA’s secrets. Harry is the first to realize that Hermione has ulterior motives and trusts her implicitly that she knows what she’s doing.
In the movies, when Harry is about to make his final sacrifice to Voldemort, Hermione realizes instantly what he’s about to do and volunteers to go with him. That level of trust and love isn’t present in any other character relationships.
6. They both experience prejudice.
Harry and Hermione both come to Hogwarts from the Muggle world, and throughout the seven books that tie is never forgotten. Many in the wizarding world sometimes forget Muggles are actually people and simply think of them as lesser beings.
Hermione and Harry understand first-hand how prejudice hurts — from being called a “Mudblood” to being ridiculed for speaking Parseltongue. Ron never has to deal with such fierce persecution, as his main “fault” is being poor. To his credit, he’s always steadfastly in their corner and no one ever doubts Ron’s loyalty. But shared experiences of persecution and hate strongly bind Harry and Hermione together.
7. Hermione doesn’t get jealous of Harry.
This point is last because it is perhaps the most important reason why Hermione should never have ended up with Ron. Ron was a great and loyal character who loved Hermione and Harry very much, but was so prone to dramatic mood swings and fits of uncontrollable jealousy that his best qualities were sometimes diminished.
Hermione didn’t care that Harry was famous, or special, or the Chosen One — she cared if he was being a good person. And Harry was never once jealous that Hermione was the smartest student at Hogwarts. They respected each other’s individual talents enough to not let them overshadow the issues at hand (see: Voldemort).