I know the advantages of vortex generators (VGs): lower stall speed, lower landing and takeoff speed according to www.stolspeed.com. So what are the major reasons most GA planes and low speed ultralights don't have VGs on their wings?
Cost. A set of Micro AeroDynamics VGs can run around $1500 plus installation cost. On my plane they are installed on the top of the wing, the sides of the vertical stabilizer (fin), and the bottom of the stabilator. I wasn't aware there were other suppliers of STC'd VGs for certificated planes. I installed mine in early 2000s, price may have gone up some since then.
They do work well, lowering stall speed while allowing the controls to be effective the same as at higher speeds. No noticeable loss of airspeed at higher power.
I've been thinking of putting them on my plane (a homebuilt). I can make them myself, but would have to figure out the proper chord wise location. I think the biggest negative to them is the care required to avoid knocking them off.
The most important reason by far is that if you design your wing (or other surface) correctly they aren't needed. Since they consume energy all the time, most manufacturers have done just that.