Ah, the age old question (which has been beaten to death on this forum I might add, but that's alright). IMO the 1.8T is quicker than both the 12v and 24v VR6's, even though the 24v makes more power. The 1.8's max torque kicks in sooner, plus it's a lighter motor. But that's just my opinion.
I can't find it, but supposedly there's a deal on eurotuner's web-site about ABD Racing taking both a 1.8T and a new VR6 and tuning them to see which is faster, but I have yet to find it.
The good thing about VR6 is that it will provide you with more power on demand anywhere on the performance curve.
This doesn't mean you will be driving faster or accelerate faster, however.
You basically don't have to rely on the turbo to kick in and supplement your engine with more air.
Here is a Theory (which could be wrong):
Let's say one dude's boost control went off the chart? The ECU would shut the Turbo down and all of us who use the 1.8T would be stranded with and engine of 1.8 Litre which would be slower then the 2.0... of course as soon as the ECU corrects the problem and opens up the gateway to the turbo, the 1.8 becomes 1.8T a vicious monster waiting to scream. All this could happen in about 0.05 Seconds which wouldn't give the 2.0 much chance anyway, but I thought I throw that in there since I was a legite 2.0 owner at one time.
I opted for the VR6, I like the raw, sick power. Are you looking at the auto or manual transmission? The only way you can get the VR6 is with a six-speed manual in the GLI (which rocks, by the way). If you want many of the creature comfort features, then you may want the 1.8T, you'll have a fast car (actually faster than the VR6 in 0-60 times) and all of the cushy stuff like power seats, etc...
What are the transmission choices for the 1.8T? Does it come with the same 6-speed as the GLI?
One other comment, the VR6's real power kicks in above 3000 rpm; I'm not sure where on the 1.8T the turbo kicks in, but I know it's well below 3000 rpm's, thus the faster 0-60 time. Test drive 'em both back to back. Let us know where you end up on this.