15 year old car with 100k+ miles will eventually have many problems. I had 2005 Audi A4 2.0 Turbo diesel and when I sold it in 2012, it had 162k miles on it. The reason I sold it was because, it needed the entire cooling system to be replaced as well as automatic windows and many electronic parts. Usually gearbox and engine are the most durable parts of the car if they are regularly serviced and well taken care of. You will have to replace many parts before it's engine's and gearbox's turn.
As for manual vs automatic. Manual is low cost maintanence in case of problems compared to automatic. However, if the manual car is badly driven, you will experience a lot of problems with the gears themselves. I would suggest replacing the clutch as soon as possible after you buy the car since it is 15 years old. It will make a smoother drive. Why automatic is more costly to fix than manual is because automatic is a more complicated and closed system compared to the manual. Also, there are more aftermarket parts available for manual transmission than automatic. (Eg. Clutch, lever, gear etc).
Also, I would like to remind you that bimmers are needy cars. You have to take care of the, well. I currently drive a 2014 X5 and I had to get the electronic components of the air suspension replaced due to cold weather. (Below -10F)