I believe Sora will be in the third installment. I just think that in some part of the game, maybe the beginning, the player will be given control of one or all of the "hunters" featured in the Secret Ending.
There are theories saying that the three hunters are actually Sora, Riku, and Kairi; all grown up and all. The Keyblades they wield sort of resemble their respective Keyblades except for minor differences which tend to disprove that theory.
The Secret Ending clues us in that Kingdom Hearts III might be about Xehanort's memory. The enemy might be the mind of Xehanort. The enemy in the first game was the heart of Xehanort (his Heartless). The enemy in the second game was the body and soul of Xehanort (his Nobody). Therefore the enemy in the third game might be his mind.