I have a MkIV wagon. Actually, two of them at the moment - my 2003 TDi 5 spd and a 2002 2.0 auto parts car I bought a couple of weeks ago for the hatch and driver's front fender (they are randomly prone to rust at the top of the wheel opening).
While I haven't driven my TDI in a few years (due to reasons not the fault of the car), driving the parts car home reminded me of how much I miss that car. I really like the MkIV interior much better than the MkV. VW set a standard with that car they've had a hard time matching 18 years later. Despite the age, it doesn't really feel dated when driving it.
Otherwise, from what I've read over the years, a 1.8T is a much better option than the VR6. For one, the VR6 wagon with a manual was an exceptionally rare car - even more so than my TDi 5 spd. To the point where many MkIV enthusiasts deny its existence. I still have the MkIV sales literature from when I bought my car, so I know it did - but I'll be the first to say I have never seen one in the flesh (all VR6 cars I've spotted and been able to look inside were autos).
Regardless, the 1.8T was in general a better engine, although like all VW's with a turbo, EXTREMELY sensitive to oil quality. Especially back in 2003 when finding the correct VAG-rated oil was not easy. A lot of guys used standard Mobil 1 (5w-30), but that wasn't really good enough until the Euro Formula (0w-40) came out. For the first 2-3 years I owned my car, I usually bought oil at a local VW/Audi dealer near work. The benefit to being so neurotic about the oil was when I pulled the valve cover off a few years ago for the 300K timing belt change, the top of the engine still looked near new.
The VR6 seems to generally be more trouble prone. Most people I know who have a sour view of VW's once owned a VR6. Hell... my own prior experience with my ex's '93 Passat VR6 put me on the defensive before I even bought my car, but I took the leap anyway. The only VR6 car I'd consider is the MkIV R32.
Otherwise... my car goes through rear brakes faster than front brakes... and front hub bearings are a frequent item. The only really electrical annoyance I've had is related to the sunroof, which would randomly open and close without control input. I "fixed" that by pulling the fuse after I once found it open after I turned the car off. The sunroof on the parts car is completely fubar and won't entirely close.
A guy on TDI-club (owns the iDparts.com website) used to track his modified TDI wagon and had no problem running with a Spec Miata run group (usually dropping).
Personally, I'd go with a 2003 TDI - it was the last of the ALH engines. The emissions controls were minimal and the engines take mods well. I've often toyed with building my car to FSP specs.
Cargo-wise, the more squared off shape of the MkIV wagon seems to haul better than the more aero MkV version. I easily fit a clothes dryer in mine with plenty of room to spare.