According to Shaga and Iris, Reshiram and Zekrom were originally one dragon who served two twin brothers and helped them lead their nation to peace and prosperity. With time, however, the brothers began to fight with one another over whose beliefs were correct: the older brother sought truth, while the younger sought ideals. The original dragon split into two: Reshiram, the white dragon of truth, and Zekrom, the black dragon of ideals. Eventually, though, they realized that both of them could be correct and stopped the fighting for a time. However, their sons rekindled the conflict again, and Reshiram and Zekrom destroyed Isshu before disappearing.
Now, onto how this relates to Kyurem. You may have noticed that it appears to be "broken"; its wings are cracked, one is smaller than the other, and its body appears frail. In addition, its base stat total is lower than Reshiram and Zekrom's; 660 compared to their 680. And, finally, unlike them, it doesn't learn an attack at level 100; however, there are two unused attacks in the game, called Cold Flare and Freeze Bolt, that appear to be intended for Kyurem and relate to Reshiram and Zekrom.
My theory is that Kyurem is the broken remnants of that original dragon that split into Reshiram and Zekrom. In the third version, it will receive a new form, much like Giratina did in Platinum, which will increase its base stat total and allow it to learn Cold Flare and Freeze Bolt. One thing that struck me about Kyurem is its species name: it's the Feelings Pokemon, which seemed utterly random at first. But now I realize that it's intended to symbolize the feelings that the two brothers held for each other.
So, here's what the game's finale would be like. N succeeds in awakening both Reshiram and Zekrom and takes them for himself. All hope seems lost, but Shaga and Iris reveal the existence of a third dragon that N doesn't know about: Kyurem. You eventually receive the God Stone (which is an unused item in Black/White; pretty clear that it's intended to be used in the third version) and go to the Pokemon League. There, you find that N has defeated Adeku and is on the brink of using his dragons' power to create his black and white world, dividing humanity and Pokemon.
The player confronts N, and the God Stone activates, awakening Kyurem. N is shocked at first, but then he realizes that it's only a remnant and he wonders if these faded feelings can possibly defeat truth and ideals. Cue...uh, something happening, and Kyurem somehow transforms into its true form. You fight a double battle against Reshiram and Zekrom and the rest of N's team, you fight Geechisu, blah blah blah, N releases the dragons for you to capture later, happy ending and stuff.
