I don't see manuals disappearing any time soon but I think Jordo! is right that they will become mainly econo-box options and hi-po cars will steadily move toward automatics and shift-by-wire DCT-type (might as well be an auto) transmissions.
But a manual can sure be a lot more fun to drive under the right conditions. There will always be the diehards that will insist on a manual, no matter how much "better" the autos have become.
