The new Beetles with the BEW diesel (so 2004-2006) were equipped with the DSG as the automatic option. Aside from the goofy shifting here and there, and the weird one-model-only drive axles that often need attention, they are OK. Certainly far better than the 01M (1998-2003) automatic option.
Note; 2006 NBs got the goofy facelift that in my opinion makes them look dumb. Squared off fenders, different tail lamp lenses, different front and rear bumper covers, etc. They just ruined the design if you ask me. So if you want one that still looks correct, and don't want the liability of the 01M, then 2004 and 2005 TDI NBs would be the one to look for. Not many around, but they are out there.