When I bought my 330Ci I struggled with the same debate. Fortunately, I had an experienced hot rodder where I worked and I talked to him about it. He told me that the clutchless manual would be the better option because I would go through a clutch a lot faster than the auto tranny and that I still had the shifting option with the auto. The auto will last the life of the car while the manual will incur maint. cost. Based on his advice I picked the auto.
My experience thus far?? Pleased...not overwhelmed, but pleased. Sport mode is great. The manual mode does protect the engine, but it still lets you hold the gear well into red line. I miss the locomotion of a stick, and you have to let up on the gas a bit for a smooth shift in manual mode. Otherwise no major complaints. It is a smart tranny and will pick gears basedon your driving style...sometimes it surprises me how smart it really is.
BUT this all just my opinion.
2003 330Ci Midnight Sapphire Black