Short legend:

Stats are "physical abilities", the player can choose which one to improve on level up (Strength, Dexterity/Coordination, Intelligence).

Skills are "knowledge abilities", which level up through use and represent frequent actions a merc can take (esp. during battle). Marksmanship,...

Perks are specialisations, that can either give bonuses to skills (think Auto Weapons (Beginner),..) or even facilitate "rule-changes" (Death from above: Increase the distance and precision with which the character can throw grenades.).