I don't believe Ford intended that the twin-turbo 3.5 liter V6 displace their range-topping 6.2 liter V8. It was to be a fuel-efficient alternative to the smaller displacement V8 (the 5.0 liter). As such, the drivetrain was given the green-washed name "EcoBoost". The market, however, decided it really liked the EcoBoost engine and sales skyrocketed. Note that the previous top-of-the-range model, the Harley-Davidson, was only available with the 6.2 liter V8. When that model was rechristened the Limited its engine was swapped to the EcoBoost. Ford now has two flagship engines which is complicating trim level decisions. The Raptor is a performance model, and as such, should come with the most powerful engine. No one is buying a Raptor to conserve fuel. When fuel consumption is removed, which engine really is the powerhouse? Ford's own Tremor package, which is designed for performance as well, confuses this further by being exclusively equipped with the EcoBoost engine.
I put quite a bit of thought into the decision between an EcoBoost model and a 6.2 liter V8 model. While similar power output means the engines end up with similar acceleration times the power delivery differs greatly between the two drivetrains. The 6.2 liter V8 provides a fairly linear power curve. It is very predictable and tractable. Power output increases with RPMs. The EcoBoost has some noticeable lag at lower RPMs. Once the turbos spool to speed, torque delivery is immediate and flat. Power output is either "on or off". This provides fuel savings but creates a less satisfying driving experience.
My prediction is that Ford will drop the larger 6.2 liter V8 and make the EcoBoost its top engine choice for the redesigned model. This will help them increase their CAFE figures and the majority of their customer base will never notice the difference. One of the reasons I purchased the 2014 Raptor was to get what might be the last of a dying breed. A large displacement V8 engined pickup. It makes no apologies for what it is. It's loud and in-your-face. One day it might be regarded as a relic of the past, of a time when people were able to drive their own vehicles, when we were able to choose vehicles that didn't need to conform to a central planner's vision of our society.