Here's some advice from a professional auto tech.
I would personally stay away from the 3.6L engine. They really don't have the greatest track record once they get some miles on them, with stuff like the left head and so forth. Atop that, changing plugs in them is a bit of a hassle with having to pull the intake plenum.
Apart from those issues, the fact is, the V6 just works too hard in a truck setting. In a Charger, a 200, or a minivan, it's normally fine power wise, but in a truck, not so much. I know a fleet locally that uses short and wide Ram 1500 Classics with the 3.6L, and they are not unhappy, but they aren't pleased either. I recently rented a Crew Cab 4x4 Laramie with the Hemi, and got better gas mileage than they get in those trucks.
Another way to consider it, getting the V8 engine is basically over-engineering your truck. How is this good? By using an engine that is under stressed, the likelihood of wearing it out prematurely or overworking it is greatly diminished. However, that extra reliability factor does come at a price of the engine, as well as potentially worse fuel mileage - I say this because your as mileage is YOU. It's all about how you drive and use the truck, so we really can't predict that.
Now, also, the bigger picture here...if you are the type to trade in as soon as the warranty expires, then by all means, get whichever you prefer. When I buy a truck, I look to drive it till either I'm tired of it, or it's tired of me. That usually takes quite a while.
My advice, go with a non-E Torque Hemi. Try to get as simple and proven powertrain as possible.