Buy what you want . . .
That said, I much prefer manuals. I drive between 15,000 and 20,000 miles yearly, most of it in city traffic, and still wouldn't have an automatic. I find that merging in fast moving freeway traffic is much easier and safer with a manual because you can downshift when you see a gap up ahead and then be in the proper gear when you're ready to slip into the gap. With an automatic, you'll only get a downshift when you floor the accelerator, and if you let up for even an instant it will shift back up and you'll lose power. I frequently transition from the eastbound Ventura Freeway to the southbound 405: lanes 1-4 continue east, no. 5 transitions to the northbound 405, and no. 6 and 7 go to the southbound 405. Depending on traffic, each set of lanes can be going different speeds and it's really good to be able to depend on the car staying in whateve gear I choose. I've done this in an automatic and it's just one hugely annoying purgatory of upshift-downshift-upshift-downshift-upshift when moving from the no. 1 lane to the no. 6.
Manuals are usually more reliable than automatics, although this does vary. My mother prefers automatics, and drives very conservatively. Her old Peugeot 505 automatic was slow as nails, but the transmission lasted the life of the car, nearly 200,000 miles. She replaced that with an Eagle, which failed after a little over 60,000 miles at significant cost. Her current Camry V-6 has over 100,000 miles in it and still shifts fine. Same driver, same location, all cars dealer maintained, go figure. One caveat: if you're not comfortable with a manual, it is easy to abuse the clutch and that can be expensive to replace.
Manuals can be difficult hard to find because dealers don't like them. When I bought my VW TDI a few years ago it was really hard to find a manual, and countless salesmen tried to convince me to buy an automatic. So far I've owned 11 cars - five Citroens, three Fiats, one each Alfa, Saab, and VW, and all have been manual. I'm not looking to change that!