I think the manual transmission is better. I don't know of any way a auto is better except for maybe convenience and backing up while towing something downhill (like putting a boat into the water). Once you get used to it, a manuals doesn't seem to be that much of a hassle. I always thought the automatic was something they invented because they though people were too lazy to learn how to drive a stick, and I probably shouldn't say this, but also because more women started driving more.
I also am not a big fan of the hybrid manual/autos that they have now for production cars. It seems like all of them have more parts, which means more things that can break, don't have a good response time, and are heavier than a normal manual transmission thus not giving you much of an advantage over a normal one.
