I really couldn't think they would eventually become something in this story, since Kyouko was not that leading character. Instead, going on through the story, she became a key character that started to grow always more and more attached to Makoto. I'm not talking of love, but surely of friendship. She was kinda diffident at the begin, but with his little willpower, his huge hope and trust in the others, Makoto won her heart and she's the one who tells him what she thinks. Makoto is not this direct and I'm not sure he understood, but I bet he really likes her since he was going to die just to protect her and her secret because she was the one who asked for that. More than once the other characters, especially Togami, underline the fact that Makoto would do everything he can in order to save her and trust what she says. It was thanks to Kyouko that Makoto menaged to survive after he was almost going to die. I think they're connected in many ways, because they menage to keep strong each other and to go on in spite of despair. I hope they can be really something in the future (and that he can grow a little, since she's taller than him D:).