It's a continuation, you have to look at the story as a whole. Sora and Kairi already had their moments of being there for one another and saving each other. Sora and Riku became a bit of enemies for a while, and there was never a time for them to reconsile, even while they were fighting along side one another. So that was their time.

And it was a tad symbolic, at the end of the first KH, Sora and Kairi were show holding hands and then they were pulled apart from one another. And the close of the KH2, it ends with their hands together. I found that far more touching than the scene with Sora and Riku (although that was rather touching itself), and that's saying a lot for the story tellers to pull that off with a mere two lines of dialogue and a hand grab.