I don't think the current 3.5 eco boost will happen in a Raptor, outside of a law by the federal government outlawing engines over a certain displacement (currently under study by our own lovely Barbara Boxer). Why?
1) Desert/heat is not a good match for turbo/heat
2) The whole "in between the 5.4 and 6.2 argument" is flawed in that the Raptor only got the 5.4 to rush it to market. The 6.2 was the intended engine for the truck and in my mind would only be replaced by another naturally aspirated V8 with more torque and horsepower.
3) My guess is the long term reliability/durability of the 6.2 far exceeds that of the current eco boost lineup.
4) More engine choices = more cost....economy stinks and is not getting better, so the bottom line is cost.
Having said that, I'd love to see as many optional engines in all ford products across the board. I like the idea of choices....I just don't think it will happen.