As someone who has commuted 102 miles round-trip dailiy with a manual transmission, I would definitely recommend getting an automatic!
Transmission notwithstanding, a 12-year-old car with 200k miles always runs the risk of needing of costly repairs. VW's are great cars in many ways, and the TDI probably has a lot of miles left in it. But when VW's break, they aren't cheap to fix.
My other concern would be for your safety. The Jetta was actually a very safe car when it was new and still holds up decently in crash tests compared to newer models. But newer cars are safer and there's less of a chance of a major failure that leaves you on the side of the road.
Your choice of a 2012-newer Honda Fit is a very good one. Most auto experts consider it a "can't lose" proposition.
As an alternative, I would at least take a test drive in a 2012-2013 Mazda3 i. It has been very reliable, has more power and room than the Fit and better fuel economy. It also has more features availalbe, if that matters to you. It's worth a look.