It depends on what your using the car for. The tdi transmission with the flexible main shafts save the first gear but have been known to shear off with very high horsepower and hard racing conditions. The regular main shafts have been known to gall first gear with similar abuse.
The 1-2 collars are problematic, mostly due to the shifter design of the C5 and B5 cars, as 1-2 collar problems are almost non existent in C4 cars. There are updated pieces which fix this issue, but you won't find a factory transmission with those pieces installed.
The later tdi transmissions (2003 and up) had a pump, standard capacity sump but the first and second gears are even shorter than the standard 01E (3.75/2.14).
Since the terms better and best are entirely subjective here are three scenarios taking into account engine and car use.
The "Best" transmission utilizing factory parts would look like this for a low displacement street car would be:
Allroad TDI high capacity sump with pump
4.11 final drive
3.50/1.89 first/second
1.32/.93 3rd/4th -- There is also a 1.43/1.07 but 4-5th spacing would be pretty wide.
.73 5th
.60 6th
Updated 1-2 shift collar parts
The "Best" transmission utilizing factory parts would look like this for a large displacment engine
Allroad TDI high capacity sump with pump
3.89 final drive
3.50/1.89 first/second
1.23/.87 3rd/4th
.68 5th
.56 6th
Updated 1-2 shift collar parts
The "Best" transmission utilizing factory parts would look like this for a track only car
Allroad TDI high capacity sump with pump
4.35 final drive
3.50/1.89 first/second
1.43/1.07 3rd/4th
.86 5th
.76 6th
Updated 1-2 shift collar parts
However there are power limitations to the stock internals, at about 600 wheel hp in a racing environment I've seen, 3rd gears shear and first gear loose teeth with drag racing.





