I would have liked to talk you out of thous groups.
Costs don't balance a super soldier.
Once one i there it eliminates ever threat below it.
That is a concept called power creep.
Imagen every standard enemy is on the same power level as a stage boss.
The Stage boss would need to be stronger than the strong standard enemy.
Thus eliminating the normal standard enemy.
To balance a super soldier it would need to have a drawback so strong that we cant use him as an easy way to end all problems.
There is also that bit about the state the insurgency (from my point of view) is currently in.
We are the guy without funding, resources or personal.
We are not a government organization or the foundation, as you said.
The Budgets of operations are cut extremely fast.
Guards are necessary, but tying our best guys to any position would make them inflexible.
But i have moved to far of point.
My challenge to you:
Write a story with them.
Show me what you have in mind.
Dose not have to be an origin story or a mission.
I might just have no idea where you want to go with this.