I have not heard of any powertrain or transmission issues thus far other than PTU seals in the transfer case. For the naturally aspirated V6's, the 3.5 is bulletproof and get's a lot of miles.
Now for the Ecoboosts, Ford did extensive testing on this motor before releasing it. They actually drove it from west coast to daytona, hooked up a trailer with a NASCAR on it, ran it 24 hours straight on the speedway in WOT (only stopping for fuel), then drove it back out west and dropped it in a baja truck and finished the baja. They also did some additional testing. I think all in all they had over 250,000 trouble free miles. It was a cool test if nothing else.
That said, this is a twin turbo with DI - historically even with BMW, Audi and Saab - a lot of carbon build up. It NEEDS to be ran; not driven like grandpa's Taurus, to prevent the carbon build up on the back of the valves, which I believe eventually will cause the turbo's to go. There is no approved Ford induction cleaning on these at this time. So run it hard every once in awhile, run premium or top tier fuels (added detergents) and run full synthetic and I think you should be good to go.
My Dad's 2011 EB has 182,000 miles on it, no issues other than regular maintenance. But that's in an F150.