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Actually, auto boxes have improved so much recently that the economy benefit of a manual is less than you might think. Some of the very latest types are actually *better* than a manual (but admittedly most of them are not very pleasant to drive!)
The problem for the auto makers is that offering a manual box option is actually pretty expensive - you need to design the box itself (or licence it in from an outside company at considerable expense), modify a whole load of things in the engine ECU to match the characteristics of the manual box, certify emissions and durability, etc, etc. If only a small number of people will take up the option then it's just not worth doing. Admittedly though, the demand may actually be much larger than is generally believed - since manuals aren't an option on most medium and large vehicles, the makers have no way of knowing how many people would choose one if it was offered.
Tony