Because of the heavy caps investment and time put into leveling up a mercenary, i have yet to see mercs make more head/eyeshots as they level up and gain more skill in it so that skill gain is almost useless minus the chance to hit at a far range. And AI stupidity can often kill mercs and a perk like toughness or an ability to kill a certain unit faster may stop that from happening as often, if you were a merc leader you would realize the time investment in leveling mercs can be high as hell and losing a 15-20k investment (a little bit later in the game since this wipe was so recent it isnt as bad) or more for BG/Energy mercs is terrible.
I'm not saying give them perks that will make them rape everything only perks that may help them out a little (toughness +melee dmg) unless of course if they reached level 21 they would be allowed to get a new skin that can use the same weapons but they get an armor upgrade (especially smallgunner ones...basic leather armor is pathetic) or until we get a combat control sheet they need some type of edge to make them worth leveling up. I don't want them to get the great perks like lifegiver, more criticals, better criticals but they deserve something when you spend a week or more trying to level up 1-2 of them and having them die or losing them in a pve battle due to them being knocked down when you leave the map or you yourself being killed.
Now that i think of it Stonewall would be a great perk for them considering ive lost quite a few that got knocked down (not knocked out) and they were trying to get back up when i had to leave to the world map.
(I'm kinda drunk again

so this post may make NO sense..if that happens ill edit it when i wake up. I like gunduz's idea and i think ill spend some time thinking about perks that are not too strong but are merc specific ones.