This was my dilemma last year when I was looking for either an M3 or 550. I eventually found and traveled about 1000 miles this past summer to purchase an e60 550 sport MT in pristine condition with only 24k miles. I have very much enjoyed the manual transmission and not regretted it once. Right now I'm in the process of doing some tasteful mods. Just eliminating the clutch delay valve and putting on a performance exhaust can make a huge difference in the feel of the car.
One thing that may or may not matter to you is that although there may be less individuals looking for a manual transmission, those that would prefer one will travel from anywhere to get it so resale is fairly decent.
You'll have a nice ride either way