I run a Ford dealer, and if the prices were the same option for option Id get the 3.5 Ecoboost in a heartbeat. I see the shop all day and all the issues people claim to have just prove the internet creates terror and fear instead of hope and joy. I very rarely see any transmission issues, in fact Ive seen zero so far, and only failed 3.5's were tuned. Dont trust the internet, as most of the stories are based on angry people. Very rarely someone will go on a website to tell how great something is, its always a place for people to grow internet muscles.
If you havent driven the 3.5 Ecoboost, you need to. Mountains of torque.