mnhead11, I'm assuming you're looking for the E39 540i, and not the all-new E60 545i, right? If you're looking for a 540i, you should decide what transmission you want based on whether manual is worth it for you. Do you experience a lot of traffic in your commute? Do you mind driving stick shift through traffic? Do you really want to row your own gears all the time?
Basically, my point is, if you want to go with stick shift, you really have to love it because that's the only way stick shift is worth it. If you only "like it", you may get tired of it quickly when stick shift's typical inconveniences show up (i.e. parallel-parking on a hill or some other difficult situation like that [fake]). And yes, you are right, most new manual transmission cars feature "close-ratio" transmissions so you will do quite a bit of rowing. For example, in my car, I can engauge 6th gear at 33mph, but I never engauge 6th that early...I am usually in 3rd or 4th at around 30-35mph and I wait until 60mph for 6th gear. Basically, these close-ratio transmissions are really great if you like to row your own gears. So maybe you should decide whether you can deal with it or not.
But to sum it all up, I must say, an automatic transmission will never bring out the engine in a car like a manual transmission does...such a better connection with the engine, so much fun to shift, such a great experience !! But on the other hand, automatic is much more practical, it is the standard now, and it is best suited to the way traffic flows here in the US.