I like the 3.6 over the 2.0.
Yes, the 2.0 is zippy like
DMG said, but that's only if it has the E-torque. The problem I see with the 2.0 is they sound like sewing machines once they hit 40K or so and sound like they're going to fall apart.
2.0 has turbo issues, I know a few that have replaced turbos before 50K miles. They also melt the coolant reservoirs, so plan on swapping in an aftermarket aluminum one.
I've got no issue with the E-Torq system other than it adds more complexity. You've got a 48v battery under the Jeep about where the rear seat is. Then there is a whole separate cooling system for that battery with coolant lines that go from the cooler up front to the battery in the back, all pushed by a small electric pump.
The extra torque when you first start rolling is nice. Wish they pushed them in the 3.6s more.
We haven't seen issues with the e-torque here at work, but we're aftermarket parts sales, not a dealership. Haven't seen issues on the JL/JT forums either, people that have them, love them.
I would love to play with one of those e-torque 48v batteries a bit for a winching application. Could you imagine running a 8274 under full pull load only pulling 200 amps?
If I was buying a 2 door, I might think about a 2.0, but would probably still go with the 3.6.
3.6s have their issues too, but they are smooth and powerful for what they are. Dirty oil can cause big issues. Change the oil frequently and keep that oil clean, clean, clean. Also install a Baxter adapter or some sort of pre-oiler to help prevent that rattle on start-up.