Having had both, for me it would be a manual but you have to weigh up lots of different aspects, type of car, type of driving, lots of stop starts etc so it would be very different from one person to the next. Multitronics can develop probs if g box oil not changed under every 40k but then again manuals can have clutch failures too depending on mileage and how they have been treated.
Dont forget the quattros have tiptronic which is a conventional auto box with a torque converter, very reliable .