A little edit of a few different things I scribbled down while trying to understand Kairi better. We know from context a little of what their life was like on the Islands before, but I wanted to get inside her head and see how she felt about the whole thing. How did we get to "Let's take the raft and go! Just the two of us!"?
When they were kids, it was always supposed to be Riku Kairi ended up with. When they played, Kairi was the princess, Sora the (sometimes) unwilling villain, and Riku was the hero that saved her. The other kids would occasionally fill in the villain role. Selphie made the best evil mastermind, with Wakka and Tidus as her henchmen. She'd clutch Kairi close and swear to protect her from stupid boys. But then Sora (now as Riku's faithful sidekick) would win Tidus and Wakka to their side, and the four of them would easily overpower Selphie and tie her up with her jump rope.
There was no question who played the dad and who played the son when Kairi wore them down into playing house. Riku was unequivocally the person for that role. Occasionally, Sora would swap out being the son for being the family dog or cat, but that rarely lasted long before they were all dogs or cats or some other animal on a big adventure together.
Playing lead quite easily into imagining - if you had asked Kairi at eight or ten or even twelve what she imagined life would be like when she was grown up, being married to Riku was always a part of the fantasy, no matter what else she imagined around it. Sora was there too, of course, sometimes paired off and sometimes not.
Things got strange once she turned thirteen.
Already mostly done with the big changes of puberty, she began to pay better attention to the boys (and there were a LOT of cute boys on her islands.) She took to disappearing with Selphie to giggle and fawn over them in secret, knowing that neither Sora nor Riku would understand. Especially since at least one of the was always a feature of the discussion.
It was a foregone conclusion that she and Riku would end up together, eventually.
Foregone to everyone except for Sora. At thirteen he became absolutely determined to beat his best friend and prove, once and for all, that he was more than just a sidekick or a lame extra in their life. He was going to be the hero.
It was this rivalry that actually made Kairi step back and check the status-quo. Riku had never seemed mean before, but he could get down-right nasty when he tried to put Sora in his place. Their constant fighting started revealing something dark in her erstwhile knight in shining armor. And yet, Sora never stooped to Riku's level. He never used the secrets all three of them knew, never assumed that Kairi would just go along with their plans and games. She was her own autonomous being to him, not some prize eventually guaranteed.
Selphie thought she was crazy when she first admitted she liked him.
"Sora?!" she she'd shrieked in disbelief, "but he's not even cute!"
"He is too!" Kairi had retorted, hands on her hips. "He's cute and nice and funny and a thousand times better than Riku or even Wakka!"
"Pshhh, please," Selphie waved a hand at her, "that little boy could never come close to Riku and Wakka's manliness. You're crazy."
"No, you're crazy. We're all still kids! 'Manliness'…" Kairi rolled her eyes, leaving the sentence to finish itself.
And then they'd decided to build the raft, and Riku had gotten stranger and stranger. She'd been so sure she loved him, once upon a time. Even when that was shaken, she'd still counted on him to keep secrets and come up with games, to be her best friend and strongest defender.
"Sora, let's take the raft and go! Just the two of us!" she'd been the most surprised of all, when she'd blurted those words. But she'd meant them.
She made her choice. If she had to pick, she picked Sora. And she would keep picking him. After all, that's what love was, right?