Okay, things I'd like to point out.
1) The cloaked person who walks down to the room is Xemnas.
2) He is not talking to himself as he walks. It is the exact lines from Mickey's flashback when we first see Ansem the Wise.
3) The cd program he uses to open the way to the "room of sleep" has 7 passwords. The first is "ANOTHER" which leads you to another screen that requires 6 more passwords. "Xehanort, Dilan, Braig, Even, Elaeus, Ienzo."
4) Though the prison cells look VERY much like the cell Kairi was kept in, Kairi was NOT kept in those cells. She was kept in The Castle That Never Was, in a hanging cell. We know this because when Namine comes to save her, they grab hands and an awesome energy comes forth from them, and Sora knows that Kairi is there. Also, Saix would not be permitted into the "room of sleep."
5) Those cells are obviously where the 6 apprentices of Ansem the Wise kept the people whose hearts they experimented on.
6) Yes, it is the Female Knight's armor and keyblade.
7) No, there is no body. It is just her armor spread out as though she laid down in that position and her body disappeared.
8) The "room of awakening" mentioned is not the room Sora was kept in in the beginning of KH2. The "room of awakening" is in Castle Oblivion, probably where Riku woke up.
9) Xemnas is not talking to a pile of armor or himself. He's experiencing nostalgia. By seeing the armor, he is reminded of the great battles they fought together. He sits in the "Room of sleep" to be alone and to just remember. It sounds silly, but everyone needs some down time to just think through things. Someone said they think Xemnas seems like more of a villain now. Well, they're completely wrong and don't know how to interpret something called "character deveopment." This scene really humanizes Xemnas.
My theory is that when Xehanort split his heart and body, his darkness went with his heart and his memories finally came to the surface. This is why he made the "room of sleep," to have a room for the Female Soldier that he could keep secret and somewhere where he could sort through his memories.
Then, he had Castle Oblivion built so he could find his other "friend."
After all of this, Xemnas decided to find Kingdom Hearts and reclaim the hearts of his friends. But he'd need help, so he recruited members into his organization, promising them their hearts back.
But when Xemnas finaly obtained Kngdom Hearts...
His heart was not there...
I beat KH2 again and I noticed that after you beat Xemnas in armor form for the first time, he says "Kingdom Hearts... Where.... Is my heart?"
Meh, just though I'd mention it.