Don't Lie

Hahaha I see.
Nah mate, I chose the "I want to understand Rin", but I ended up failing so fucking bad. And I chose "I want to support Rin" to get a good ending :D
After all 3 route I've done, the hardest one is Rin, I've done Emi, Rin, and Hanako.

Misha dies at the end, right? Her hair is actually a wig and she had cancer, and by the end of the year she's dead.

I just get the feeling she leaves Hisao and Shizune permanently somehow, and with a character as bouncy and lovable as Misha, often that departure is written under a tomb stone.

Dear Hisao,

All you had to do was love her. Love her with everything you had. In the end, all you are is someone standing far away, watching. Why didn't you tell her none of it was her fault? That it was perfectly fine to be who she was, and that that's why you love her? That despite that, you can still come to understand each other, and love each other? In the end, all she wanted was someone to understand her...that way...she wouldn't have to feel so alone. She's unsure of herself, she's clumsy with her words, and the things she does...she's still finding herself...all you had to do was be a constant lighthouse in her fog-filled sea. She figured out that it's okay to be herself...but she did that on her own. She's still alone, Hisao.

picking up Rin's bra after they've gone all the way. Hell, he even starts getting scared shitless right before they do it, comparing himself to the stories of old people who have heart attacks during sex. Of course, Rin is there calm him down.

Hisao has intimacy issues even after they finally go all the way, so he finds it difficult to say he loves her, especially after she just bluntly asks him. Rin, on the other hand, had only ever known the merits of a friend, and though Hisao wanted to be more she was afraid. During the H scene, she asks if he doesn't want to be her friend, and then says something to the effect of "It would be alright if you weren't, you know".
In the final scene, Rin tries out what it would be like to love as others do, but finds it "tastes funny". The love she and Hisao share isn't totally conventional, but they do adore and cherish one another.

You have to keep in mind the two main themes aside from the theme of change present in the Rin Route: understanding abstract art and proving you exist.

1. The Art of Rin: Rin is abstract art for Hisao. He becomes pretty obsessed in his infatuation with her and trying to understand her, to the point where he rarely even speaks to anyone other than Emi and the Student Council Duo (when he has to). In trying to understand her, he begins falling for her, but also begins putting his own idea of what she should be onto her, as the art teacher did. He tries to change their friendship into a romantic intimacy at the wrong time, which is only made a wrong time due to his insistence she take on the exhibition. The pressure of his projecting what she should be, her teacher projecting what she should be, and her trying desperately to understand herself push her over the edge and confuse her. Hisao confuses her own confusion for being an emotional cock-tease, and only realizes what he had been doing to her when he sees himself in that asshole teacher who was only trying to live his dream through her.
_In abstract art, like Rin said, there shouldn't be a name since it is abstract for a reason. It presents itself. It is what it is, and should be accepted and enjoyed for being so. Though she understands the concept wholly, she never applies it to herself, instead turning to her art as a means of understanding herself. She becomes so frustrated at how everything has turned out and how little was accomplished and screams and cries. Hisao even admits that his affection for her makes him unable to be the friend she wants and needs him to be.
_However, in the end he realizes that, though the mental fog she lives with is something he will never be able to see through fully, though he will never be able to see into her soul and understand her the way she wants (which is an impossible desire), he does love even the most frustrating parts of her. He accepts her for who she is, as does she, and like a person fascinated with a piece of abstract art, he watches her as he always has.

It was clever since the reason why most would go for her is just how unique she is. Who knew her story would be all about that as both a defining trait and her key disability?

2. Proof of Existence: Hisao early on resigns himself to an early death despite there literally being tons of advancements to be made and being made to help him live a long life. Rin also resigns herself to the fear of one day dying, but mentally, stating that she feels she's slipping away. Part of her disability isn't just the mental fog, but how much that fog encompasses. She's clearly not mentally deteriorating (if she was she'd be less unique and more...brain dead). However, her inability to understand even herself, her inability to convey her emotions the way others would, and her bit more than slight ADD convinces her she'll one day fade away. Thus, she paints in order to leave proof of her existence and hopes one day someone will come along, see into her art right into her soul, and understand her completely.
_By the end of the story, Rin has not only finally opened to the idea of being in love with Hisao, as scary as it is for her, but also accepted that she's just an enigma, a puzzle to never be fully be put together. The emphasis on "present" shows not only that these two are living with each other for the moment, but also that they aren't going to worry over the future, something Hisao had been doing for quite some time.

Of course, two other things arise from this: 1) They may not have a clear goal or future (which is stupid to those with mature minds, but acceptable since they are just 18), but they will stick together, and 2) The part when Hisao surprises her with a embracing kiss alludes to the idea that he won't die early and they'll be together (the fact his heart and hers sync up)

I can see why you thought they didn't work out at first. With how he doesn't return her "I love you", how he seems to mention the idea of needing to ingrain this moment in his memory, and how the final image is of her and not him, it can easily trick you. But don't be fooled, since that is only because Rin's story is less about the love Hisao and Rin share (unlike some of the other KS stories) and more about Rin finally coming to terms with who she is and not looking to others to tell her such.

Hisao and Rin make it. It's not as obvious as some other endings, but no worries.