Depends which model you are going for? Petrol or Diesel.
Also your daily commute, are you sitting in heavy traffic daily?
I personally went for a manual as I prefer the interaction and control you have with the vehicle, even though its a diesel ie. 320d. I enjoy it as I don't sit in start stop traffic a lot.
Also, have heard of quite a few issues with the e90 auto boxes as they age and have not been properly maintained. As well as electronic issues.
A manual box will require a clutch and dual mass flywheel change at some point so you will need to budget for that.