In my opinion, manual transmissions are usually better than automatics. Manual transmissions, when not abused and driven properly will be a great transmission. Some of the man trans now-a-days are stated to be maintenance free, but you still have to change the fluid. Manual transmissions are also the only direct connect between your engine and your wheels. If something breaks, it is usually easier to fix. Don't downshift a lot either...its wears the syncros a lot faster as well.
Automatics can be fun, but if they are abused enough, they jerk when they switch gears and can overheat since they are larger (although they disapate more heat) Automatics usually weigh at least twice as much as a manual, as well.
Personally, if I lived in a city, with really bad stop-go traffic, I'd consider an automatic, but there's no high like driving a manual transmisison. The long term and short term benefits depend on what you are looking for. If you are looking for a "stress-free" drive in traffic and are willing to sacrifice a little bit in gas mileage, go for an auto. If you want to be able to have fun, not have another computer controlling your life/actions, and have a little better MPG, I'd say manual.
Of course, it seems as if a few auto trans are being geared to get better MPG than a manual (i.e. TSX). A manual transmission will cost you less over the long and short run (autos require more fluid and filters, and usually cost upwards of $1000 to opt for it).
Remember that this is my opinion