@tycobb: All the cons for a manual transmission are associated with human error.
Driving in traffic can be not only a nuisance but physically taxing after a while. I'm sure you are fine with going 1-2-1-2 every few minutes but after an hour of that I don't care how awesome anyone is at driving stick it will definitely be more annoying than if you're just feathering your brake pedal once in a while.
You are a lot more liable to damage your own car through spotty shifting, unlike an automatic where it's literally impossible to damage the transmission on your own accord. Once again mileage may vary depending on the driver. You may be skilled at shifting, but not everyone will be even if they think they are and will eventually wear out the clutch because they thought they knew when to change gears best.
Objectively (ho hum) it is much safer to drive with both hands on the steering wheel at all times and only having to concentrate on gas and brake. After a while anyone used to shifting will tell you it's second nature and they don't even think about it - but you are having to fiddle with pedals and the shifter every once in a while which while giving you more control over the acceleration of your vehicle is also taking away a small degree of mobility from being able to steer.
Depending on where you live a manual would simply be a bad choice to have. San Francisco is extremely hilly and not the best place for manuals. You are a pro driver and can start from a dead stop on a sharp incline no problem but it is still more problematic than an automatic.
Overall the con is that you are doing a lot more manual labor to drive your motor vehicle. The trade-off for every day transportation in an urban environment is negligible as how important is it really that you shift from 2nd to 3rd at the perfect moment when there is a red light coming right up, or a school zone, or any other city based element that make fast acceleration pointless. Instead of driving the car you are concentrating a lot more on making the car function which is superfluous for regular commute to work. If you are an ice road trucker and need to really control your differentials because you can slip off the road and die then I fully agree - but when you're driving 5 miles to the office and stopping at a red light every minute, dood who cares.
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