Hard question,
If you are comparing a W203 and an E46, I recon motor wise they are probably the same.
Gearbox I am also going to say the same, as its driving style that kills these boxes, not the gearbox itself, altough i think merc will have a stronger box the the GM box your going to be putting in.
Interior and trim wise, I recon the merc is going to hold out better in the long run then the BMW,
Parts on the merc will be cheaper as well actually, Rick540 proved this.
However, all of this said, I would still buy the BMW. Remember, that turbo's and injectors are maintance items on these cars, some last the life of the car, but they can go in any vehicle at any time.
True there were bad batches of turbo's on certian 320's when they just came out, and somebody like VW has much more experiance with turbo charged vehicles then BMW did at the time, but issue has been sorted.
the 330d or M57N2 is probably the nicest diesel motor in existance.... imo of course.