Road Bikes: Aero vs. Traditional
GC leaders are generally not out in the wind by themselves or taking many pulls on the front. They often put time on the field on climbs and in individual events like TT (which use bikes focused on aerodynamics).   As such, in pack riding GC leader will likely favour a bike that focuses on climbing (light and stiff) and handling (note, aero road bikes are improving here), rather than raw aerodynamics.  GC leaders are also more likely to be conservative with gear selection because they are in it for the long run and can't afford any technical issues.

That said, aerodynamics still plays an important role within the pack while drafting. As aero road bikes continue to improve (e.g., less weight penalty) and continue to prove themselves in competition you may very well see GC leaders riding them soon.