There were some issues with early models of Atlas which VW has addressed. So far I have not heard or seen any issues with the S 2.0 model. The only thing was the ding when the key is left in the ignition was not happening but a software update fixed the issue. Push button Start models were not part of the TSB.
it all comes down to what you need in an SUV like this
either a-to-b driving with fuel economy as priority or more capability to haul a lot of passengers and/or cargo
I fall into the former part although I wish power was increased
Well the 2.0 can tow 2,000 and the 3.6 can tow 5,000 so unless you have a giant ski boat to tow the smaller engine will do fine and still haul a bunch of people and still get better mpg while doing so.