It's obvious from the opening scene that the idea of imprisoning horned youths in this castle is a tradition which has been practised for generations. There are dozens of sarcophagi (if I may call them that) around the room in which our protagonist begins his explorations. I feel compelled to ask why, although I don't think it is possible to come up with a definitive answer. The best I can do is to suggest that the life force of horned boys is drained to provide the queen (if I can call her that) with energy to extend her own life and provide her with power for manifesting her magical abilities. It is unclear why Yorda exists, too. Does it seem that the queen engages in procreation? Doesn't seem likely to me, she appears to be a magical creature. I don't doubt that she could easily create Yorda, but... for what purpose?

I think the basic plot premis is a little clearer once you take Shadow of the Colossus into account. At the end of that, the hero goes all demonic, the bird comes back to life and you see her with a kid with horns (If memory serves), implying that Ico is in some way decended from the SotC kids. One would assume therefore that kids with horns are direct descendents of the SotC people and therefore, have some magnitude of that demonic power. Chances are, it's horned kids who have the power to defeat the witch, so she gets the villagers to lock them all up in her castle, either just to kill them or so she can drain their horn magic or what have you. Yorda is probably some sort of Ying to the witch's yang, an opposing force that she needs alive to live herself but who has the potential to overthrow her, so she keeps her locked up.

That's all conjecture of course but it looks like the kind of standard fantasy story schtick the Japs are fond of. I think part of the joy of the story though lies in it's ambiguity. Much like SotC, there's obviously greater forces at work but the focus of the main character and as a result the focus of the player is on immediate events. Ico doesn't knw why he's been locked up and so neither do you. SotC boy is only concerned with saving his missus and so are you. I don't think a long and detailed back-story would enhance either game at all, if anything you'd lose focus on what you were doing and start concentrating on the wider plot, lessening the intensity of the experience. In a game with a strong narrative like most Final Fantasys, there's no ambiguity, you know you're the hero, you know there's a bad guy to off and the fate of the world rests on your shoulders. In Ico, for all you know the queen is just a nonce who likes fucking dead children, there's no grand saving the world bullshit, you're just a kid trying to escape from a castle, being slowed down by a girl with downs syndrome who you need to drag along to open doors for you.

The reason films made from books are always dissapointing is that when you read a book, your imagination fills in the details of the setting and the voices and the look of the characters, no matter how detailed the descriptions. Once it's put into a film, those things are someone else's interpretation and bound to differ from yours slightly (Like who the fuck pronounces Sauron as Sour-on, rather than Sore-on), you lose connection with the story. Ico and SotC leave a lot to your imagination which is probably why people tend to find such a connection with the games. I didn't really enjoy Ico that much but SotC is an incredible game and from a story telling standpoint at least, they have a lot in common.