There is a great shift that you mention that occurs in AI after the boy gets to the bottom of the sea. I agree that there was a whole different feel, but that didn't detract from the movie because the shift occurs at the point when humanity suddenly disappears and a whole new dimension arises - the whole human world that has been disparaged and turned upsidedown in this alien environment. Leaving the boy at the bottom of the sea would be like creating another Brazil (original ending) or director's cut of Bladerunner. But Spielberg, provided a holistic touch, otherworldly spin on the whole movie. And still the ending remains ambigious when the boy sleeps - what happens then?
I liked William Hurt's character disappearing because here the reality of humanity comes full front and center and it becomes clear what lies beneath the veneer and plaster of real mankind. This Kubrick touch was great, sliding humanity into a darkened portrait, giving Hurt's character a more complex character than the ordinary movie character that audience have come to love and enjoy.
And as I mentioned the clownish artificial persons really represent the humans who created them, they became bigger than life, they become the exaggeration of humanity while humanity degraded into even more distorted, twisted characters themselves. Thus, the whole behavioral ludicriousness becomes so marvelously tied together and integral to the movie's intent.
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