Not many TDI's came with DSG's...2005 and 2006 only right?
I HAD a TDI with an autotragic as it has so nicely been renamed. And it is just that, tragic. The 01M I think overall is a decent transmission....for 2.0's and maybe 1.8Ts, but the torque in the TDI I think is what kills it so prematurely.
I HAD 150K on my autotragic. Almost immediately and VERY quickly...it died. Had to swap in a 5-spd. I LOVE my 5-spd. I would not want to go back to an automatic EVERY. MPG has increased by almost 7mpg, and that's not including long trips yet!
The power is a lot more usable with the 5-spd than it is the automatic.
Now here is a thought to consider....buy an automatic TDI....save for a swap. You can contact JimBote on the TDIclub and he can do a 5-spd swap for about $2,500 parts AND labor! He'll even find the parts for you! Now you could always get a better or new clutch/flywheel/etc and that would be a little extra to his starting price, but you get the idea. Then just wait for the autotragic to crap out, or come close to crapping out and swap it!
I love my TDI now that it's a 5 spd. I have the larger injector nozzles, the automatics come with the larger fuel pump already, and then toss in the power of a 5 spd, trust me, you'll be the envy of other 5 spd TDI-ers. I've heard everyone tell me they are jealous because they want the 11mm fuel pump...that comes standard on the autotragics.
But it's up to you. I enjoyed my TDI as an automatic, but I LOVE my TDI as a 5 spd.