Yes same skills doesn't stack... But at this skill is something special... Let me explain.
I have a hero and a merc with 100 points at every attribute, same and my enemy. My skill is leadership and my mercs is battle cry, both max level... My attributes will be 124 and my enemies attributes will be 76. This is like they stack!!! the difference is 48 points! same effect as stacking... The same can apply to the mystic's skill the light one give +1 skill point to every one at your team and the dark gives -1 to every one at the enemy's team.