I have always felt I had better control over a stick shift. In fact you are in full control over deciding when it's time to switch gears (right or wrong), but I just sensed I was better at deciding than an automatic. I would end up with an automatic when I would find the right buy on a second hand pickup, but with a new car I made sure it was a manual. And of course the gas mileage was always better. BUT....
These arguments may be less valid than they were at one time. Some new cars are actually posting higher gas mileage on their automatics, with all other things being equal. Can you trust the the gas mileage claims? Probably not, but if that's the case, I would think the ratings would all be inflated by about the same percentages on all vehicles.
Sooo... I bought a new car just this year, and I changed over to an automatic. I had a one week "test drive" that was loaned to me while another vehicle was in the shop, and I was impressed enough to buy that very same loaner car when the dealer decided to sell it. Gone is that radical neck snapping surge when an automatic shifts down on an uphill grind. I can't do an actual gas mileage comparison, because the car has a much bigger engine than the economy engines I've demanded in the past. It's 10 mpg less than my old Mazda 3 trade in, but it's totally different kind of car.
I also own a Mazda Miata. It's my second one, and if I buy a third it will always be a manual transmission. It's seems like putting an automatic in a sports car would be sacrilegious. It would be like watering down your milk. For a regular car, newer more modern automatics may be adequate from now on. I'll know better a couple years down the road with this new one... maybe.