Interface metaphors will remain 2D until we have inputs and displays that aren't 2D.
As for "Minority Report"-style interfaces, I cringed really hard when I saw those "wave your hands in the air" interface scenes in that movie because I knew that people would latch onto that as some kind of wave of the future. That kind of interface is horrible for most things.
How many hours a day do you people spend on the computer? Eight, ten, twelve or more? Waving your hands around in the air is really, really tiring.
It's like everybody has forgotten the failure of light pens already. In the 70s and early 80s, everybody thought light pens were the ideal way to work with computers. They mimicked the pen-and-paper thing everybody already knew, and there was a direct 1:1 correlation between the movement of your hand and the "pointer." What wasn't to love? As it turns out, light pens were actually awful to use and the mouse became the dominant non-keyboard input device. They were physically tiring to use and required expensive displays.
Anyway, discussions over input devices and UI metaphors are really missing the point anyway. The problem is not that we can't point to things quickly enough, or that we need to do things in 3D, or any of that.
The problem is that we have too much information to sort through. How can a system - regardless of interface - help us to find the information most relevant to what we want? In other words, interface is important but the REAL issue isn't how we get stuff into the black box or out of it. The hard part is figuring out what to do inside of the black box, and that doesn't change whether you're doing things in two dimensions or fifty-seven dimensions.