I think it comes down to how much painful driving and also how it married with the engine. I was only going to buy a CS in manual but would never buy my 330d in manual ( you can't anyway ) but the big lump of torque and 8 speed auto is a match made in heaven .. but if I went for something like an M140i or Golf Gti I would go manual for the driving experience ..
Down to personal taste, if you are happy to stump up the cash and the type of driving you do mostly. All these modern auto / dsg boxes are pretty cool, in my 330d it knows from the sat nav where the junctions and sharp corners are and shifts down just before them.. Unreal really !