I just picked up a VW Golf wagon with the 2.5L, the premium for the tdi, maintenance (DSG fluid changes and timings belts) and other potential problems were not worth the better gas milage. Unless you get a manual or do all your car maintenance yourself the cost of timing belts and DSG fuild changes wipe away your savings. On top of that there is the potential for a hpfp failure, if you live in a cold climate your intercooled will ice up and hydrolock your engine and there are issues with the exhaust flap and regen cycle. I could have ended up with a TDI without those problems but I didnt want to risk it, if you can get your hands on a older tdi with low miles I would go for it. I had a 96' jetta turdo diesel and put 500k km's on it before te body rotted out and my dad has a 01' tdi with 600k km's on it still going strong.
I loathe, I mean LOATHE, the 2.5L engine. It is an abomination. Sorry, that would be an absolute dealbreaker for me.
Also my wife's 2000 tdi jetta is a manual, but otherwise fully optioned GLS, right down to the Monsoon branded sound system with the 5 disc changer that could do suffle mode across all 5 discs. Seems so antiquated now, but that was a pricey option back then.
Anyway, she would never drive any car, but especially a TDI, unless it was a manual. Which is why we were so excited for the 2015 Golf Sportwagen. As far as we have been able to tell you could not buy a manual TDI JSW with a sunroof. They just did not make them. Early reports are that it will be an available option for the GSW (6 speed).
Oh and we live in a warm climate, so all those cold weather concerns are also not an issue.