It's helpful to remember that any dissipation in exhaust restriction would be best aided by a lessening in intake restriction...that's why Joe shmoe who throws a K&N on his ride and expects to go rocketing on down the track will likely be sorely disappointed. I played this game in high school and didn't get it until I got into the higher maths and physics...It's funny when you see the Toyota commercial running right now where they tout the excellence of the factory shorty headers that they use on the (???) Tundra, while their intake tract has the aerodynamic efficiency of John Wayne's large intestine. Love to see if the rest of the engine was tuned around them, tho (they do weigh less, at the very least)...
Eventually when you boil it all out you get down to the camshaft; therefore, you can start there and work out, or start at the outer end and work in; regardless, it all has to work together, or you may wind up with negligable power gains.
This always does not hold true, however. Some cams are naturally better than the rest of the breathing mechanism, and some intake and exhausts that rock are hampered by a cam that's designed for Grammy Smith. Ever see a 76 Duster 360? Dump the intake and exhaust and you're in the 13's with minimal cash outlay.
When considering the difference, other than weight, the difference is akin to the difference between a rifle and pistol. Everything varies by degree, but this is a decent generalization, at least as far as my stupid physics textbook says. What does everyone else think? What makes the difference with the 4.0, for instance? Intake, exhaust, valve timing/duration, or what?