What about this: Separate 0-100 scaled attributes from less important attributes. Make the less important attributes based on something like "profficiency" levels. Probably expand the remaining 0-100 scale based attributes.
One problem still is, that certain attributes/skills are incomparable with others concerning their importance - like medical vs marksmanship. Why not to create another group of merc properties?

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"Soldier's composition"
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---- Experience: ----
Level 1-10
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---- Attributes: ----
Health 0-100
Strength 0-100
Agility 0-100
Dexterity 0-100
Perception 0-100 (Focus, good eyes, ears; affects shooting, interrupts, lot of things))
Wisdom 0-100
Marksmanship 0-100
Leadership 0-100
---- Can be profficient at: ----
Medical 0-3
Explosives 0-3
Lockpicking 0-3
Repairing 0-3
Stealth 0-3
Driving 0-3
Survival 0-3
Discipline 0-3
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Explanation of profficiencies:
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Medical:
0 : Cannot bandage or doctor, an attempt more likely ends in harming the victim, or draining the medical kit pointlessly
1 : Can bandage (not dying) mercs, but not self, mediocre speed, bandaging cost certain amount of energy, a tiny chance to hurt the patient on the process
2 : Can bandage anyone, even dying soldiers and self, good speed, bandaging also returns some energy to the patient, can perform doctoring assignment, but it's exhausting
3 : Improved bandaging, improved doctoring assignment which do not cost so much energy, can do doctoring at hospital facility

Explosives:
0 : Handling explosives usually reslutls in failure or detonation (except grenades, but there is penalty for them too)
1 : Can set simple mines, throw grenades normally
2 : Can place mines and bombs normally (door bombs included), can attach detonators (with penalty)
3 : Can disarm bombs and mines, can create detonators from nightwatches and wires, no penalties when handling explosives

Lockpicking:
0 : Cannot lockpick anything at all, only examine doors for traps
1 : Can lockpick low level doors, but not electronic locks, lockpicking makes a lot of noise and costs some energy
2 : Can lockpick any non-electronic locks (no noise, no energy cost)
3 : Can untrap doors, lockpicking gets better, can unlock electronic locks

Repairing:
0 : Cannot repair items at all, an attempt results in damaging the item even more
1 : Can only repair (non-electronic) items with 60+% status to 90% status, with repair difficulty -1 or easier, slow speed
2 : can repair items with 30+% status to 95%, with repair difficulty not under -4, electronic items are very slow to repair, otherwise normal speed
3 : can repair items on any status to 100%, also vehicles, can merge items, fast speed

Stealth:
0 : Cannot move silently, camouflage has 50% effect, moving reduces camo/cover effectiveness drastically, makes more noise overally
1 : Can move silently with a penalty, and it drains more enrgy, camo has 70% effect, movement reduces camo/cover effect a lot, makes normal noise, but certain actions are still very loud(running, climbing on/off roofs, jumping fences, swimming etc)
2 : Silent movement is at normal (except running), cost normal energy, camo effectiveness 90%, movement still reduces camo/cover effectiveness significally
3 : Can kill completely silently (bare hands/knife), camo effectiveness full, cover bonus, movement reduces camo/cover effectiveness only a bit, can run silently

Driving:
0 : Cannot drive vehicles (needs different merc with Driving)
1 : Can drive at mediocre speed, has a chance to damage the car sometimes, cannot drive offroad
2 : Can drive normally, although if driving off road the car is damaged from time to time
3 : Can pilot helicopter (muhaha), and everything drivable, even tanks, speed bonus, no vehicle damaging

Survival:
0 : Loses a lot more energy when traveling outside cities, sometimes get even slightly hurt, can regain energy only to 60% status if sleeping in the wilderness
1 : Loses less energy when travelling outside the cities, can regain energy only to 75% if sleeping outside
2 : Loses energy normally when travelling, can only regain energy to 90% if sleeping outside
3 : Can regain full energy, also helps others with lesser Survival in the squad (reduces slightly their penalties)

Discipline:
0 : Enemy shooting scares the shit out of you - suppression is very effective on you, morale cannot go higher than 70%, all negative features of your personality and disability have higher effect, if hated merc in the squad, you screw everything up
1 : Suppression has still high effect for you (but not as with zero Discipline), morale can go to 85%, negative features of your character have normal effect
2 : Normal suppression effect, morale can go to 100%, practicing/student assignments go faster
3 : Has suppression tolerance bonus, all positive features of your character are higher, bonus to training militia

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---- Effects of Skill Traits: ----
Generaly Skill Traits would remain almost the same, or at least their core. Certain proficiencies would get bonus from Skill Traits, and certain Skill Traits would have minimal proficiencies to be picked up (minimal requirements).
Paramedics need Medical at least 2, Doctors at least 3..

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---- Gainig proficiencies: ----
The best way I have in mind, of how to gain proficiency is to learn them directly in the game at certain Facilities. But for that, you would need a Free Proficiency Point which you gain every time you level up. Some free proficiency points you gain at the merc creation of course. You could also gain proficiency points for completing certain quests!
Example:
You have Level 1 merc. He has 5 points in proficiencies - let's say: 2 Explosives, 1 Discipline, 1 Survival, 1 Stealth. We would like to obtain Explosives proficiency of 3, but on this time, we have no "free points", so even if we find the apropriate Facility which can give us the desired proficiency, we cannot learn it (we do not have the learning capacity for it now).
Now we gained a level, becoming level 2 merc. To our Free points, one point is added. Now we could use the point to learn a proficiency. So we put ourself to the Facility and choose "Improve Explosives Proficiency". After a certain time, we get a message, that we gained the proficiency level, and the assignment is disallowed again.
We gain another point at level 2,3,4,5.. then two points at level 6+. It's an example, the amount would be externalized.

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Well, of course the game mechanics would have to be rebalanced. This is a very rough concept, just what came to my mind now. There could be more levels of proficiencies.. or not.
If anyone would like this and be enthusiastic enough.. All this is within my capabilities. I would need help though. Mainly it would have to be worked to a very good concept.