There is a reason Ford went with 2.5's. They handle off-road terrain decent enough for the majority of people and they are cushy on the road. 3.0's is a big step with your suspension and when it's coupled with the other mods generally associated with 3.0's (UCA's, Tie Rods, Rear Springs, Bump Stops) you're getting closer and closer to making your truck a race truck (obviously not a race truck, but you get where I'm going with this). 3.0's aren't designed to be super cushy on the road, especially the ones Raptor owners buy. They are designed to allow you to go faster off-road and take even bigger hits than what the stock setup is capable of.
If you're OK with that, 3.0's are great. If you want cushy ride, 2.5's and progressive springs all around is the way to go. At least this is the way it's been explained to me by a handful of people.