You're right, some of the 3D colours do look very dark and muddy. That shot from the amber mine almost looks sepia!

I agree that it's hard to accept that it ever looked this way theatrically. The film stills do have a more brown look but not to the extent of the 3D BD. But if those aren't the theatrical colours then I have no idea why they went with such a radical change. Surely you wouldn't want to deliberately darken a film for 3D considering that 3D glasses already make it appear darker?

The LD colours may well be a happy medium. How does the T-Rex attack on the jeep look in the LD? The 2D BD has an overwhelming blue cast to it whereas the 3D BD has more natural colours.