Well the decision between the VR6 and 1.8T pretty much comes down to this:
VR6: Better if you want to keep it stock or if you have lots and lots of money to modify with.
1.8T: Better if you have a modest budget to modify with. For example, with just one mod, a chip, your 1.8T will have more power than the VR6. But as you can imagine, you could put a turbo on your VR6, and there is pretty much no comparison.
Ahh yes the never ending topic of VR6 vs. 1.8T. I hate to say this but I have to when I see these posts. Try using the search you will probably find 100+ topics on this. Also read a few threads in the MK4 forum to give you an idea what you are heading into. Best of luck!