My daily (soon to go to my son) is a B5.5 1.8T 5-speed Passat Wagon. It's a great car.
I get to drive two MKV/VI JSWs...a DSG TDI and a manual 2.0T... No complaints with either.
The wife has a 4M B6 wagon. She likes her car.
Hope that establishes some credibility. So here goes.
If you want a new VW wagon in the US, you're buying a JSW and you've got two choices that affect the drive: engine (TDI or 2.5 gasser) and transmission (manual or DSG).
They are both good engines. The 2.5 is the simpler engine, but the fuel mileage isn't as good as the TDI's. IMHO if the choice is about overall cost with long-term ownership, the 2.5 is the safer bet. If you're short-term...three and out, go TDI. But drive both, because your reaction to the engines matters. I'm also careful to use the gasser for short trips and the TDI for anything over half an hour. Diesels work best if they warm up, something they probably won't do on very short trips.
They are both good transmissions. Manual will surely be cheaper to maintain over its life. The DSG is way better than a slushbox like you find in nearly all of the Passats (some newer B6s have DSG vice Tiptronic). I prefer the DSG in traffic, the manual nearly anywhere else.
If you want 4Motion, you're going with a Passat. There were some older Passats with 4M and manual--these are really, really rare. All B6 4Ms and most B5.5 4Ms were automatics.
I like the B5.5 Passat's form factor a lot. It's slightly wider than the current JSW, with better passenger foot room and close to the same trunk size. I like the 1.8T engine over the V6 (which is not a VR6) and the manual is much better than the automatic. The downsides... they're old and they have a few maintenance issues that can bite you if they aren't kept up with.
The B6 Passat is a step up in size and in luxury from the B5.5 and from the Jetta... depending on how it's equipped, of course. (The wife's car is loaded.) Reminds me the most of our old E39 BMW wagon. Best rear passenger room for length. Width is a toss-up between the Passats, but both are definitely wider than the JSW.
If you're looking at a used JSW, get a gasser. The 2009 2.0T is a GTI with useful cargo space, but they are rare, but a hoot to drive and well worth the trouble of hunting down. The 2.5s depreciate much quicker than the TDIs. That doesn't make them a bad car, it makes them a great deal. Because all TDIs are pretty new and have high resale, I'd just buy a new TDI since they are so close in price to used TDIs.