I saw no difference from having dual 3" pipes exiting right underneath the Quad Cab Door, to going to Dual 5" Stacks exiting 12-16" above the cab.
5" to 6" stacks will help reduce EGT.
A few downsides,, They are higher Maintanence,, you will need to keep them straight,, plastic bags, or cups can't be laying around in the bed, or they could touch the stack and melt (Makes a mess), a soot shower on startup. If you run alot of fuel (smoke) through your truck, the problem will be worse.
I'd say go with the stacks. They look too cool. If they are straight piped, the drone inside the cab can get pretty obnoxious.
My opinion,
Merrick