One great advantage to a manual transmission is that if the clutch wears out (which it ought not to do until about 120,000 miles if your clutch technique is correct), replacing a clutch is a HELL of a lot cheaper than replacing the friction materials in an automatic box, and, indeed, if there is significant residual material in the fluid in an automatic box you may have to condemn the box.

Correct use of a manual transmission also means that you are driving the car in stead of the other way round and in critical situations that could mean you stay in motion or on the road rather than otherwise, and possibly alive.