I admit, when DS was that age I completely agreed with you. I kept wishing for the "good old days" of my childhood when the only "special pieces" were doors, windows, and wheels. The new kits seemed like a nightmare to free build anything. How to make all the special pieces into something other than what the directions specified?
But this year, DS (7yo) had some $$ from Christmas and bought a bunch of kits. At first he just wanted to build based on the directions. But then he had a "battle" and destroyed all the buildings in a big jumbled mess. So he started free building and so did I. We started challenging each other to use the specialty pieces. We started going to the Lego store to look at free form things they had built and started noticing that there were multiple cool ways they had used specialty pieces. So now we are having a fantastic time. It is still difficult to figure out how best to sort the pieces so we can find what we want but here is our latest method: 8 shoe box size clear plastic bins with lids labeled as follows: flat bricks, full height bricks, roof pieces, base plates, specialty, windows/doors/walls, wheels/tires/axles, finish pieces. Then we have 3 smaller containers with lids that can fit inside those bins. These are used for sorting out really tiny pieces.
Now I like the new Legos and we shop for kits based on what cool pieces are in them that we think might have lots of new uses :) So building the kits is a good way to learn ways of using the axles, gears, etc. but once those "lessons" have been learned your son can go crazy coming up with unique stuff.