Don't Lie

So, in the end, it didn't work.
Damn it! I almost cried!

Im on teh interwebs and i have no idea of wats going on!!!

But seriously what's all this about? Is it a game based off a manga or something?

What? How did it not work, mate?

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.

Was it when you had a choice after the first H scene with her? After you find her at night in the artilier(whatever it's called) doing that, and Hisao gives her a hug? The choice scene in the argument the morning after, I mean.

The good ending is her standing in a field of dandelions asking you what the word for feeling like everything is going to be alright is

Remember in Rin's route how Hisao said that he wants to get closer to Rin but feels the relationship is fragile and that every time he gets closer he is afraid of them splitting up. You get that same kind of frustration with Hanako but in a different way. Won't say more for fear of spoiling the plot.

What? How did it not work, mate?

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.