I guess I should probably ask what your goals really are.
If you are planning on going balls out race car status, it will be cheaper and easier to go 1.8T.
If you want a car that you will throw basic mods on and enjoy, 2.0T all the way.
The 2.0T FSI cars have a HPFP follower that needs replaced somewhat regularly (20-25ksh) for most lightly modded cars, but is easy to do.
The Auto's really suck the life outta the car. Drive a 2.0T 6MT.
If you want to drive a 2.0T w/ Flash & Downpipe let me know.. Mine has coming up on 140K and it's been awesome.