So in my current playthrough, I've gotten hung up on the idea of creating a small squad of supersoldiers by cloning them through QE, enhancing them through Expanded Prosthetics and Organ Engineering, and equipping them with bleeding-edge weapons from Rimsenal and UNSC Arsenal.

One addition to QE that might really drive the supersoldier idea forward is the ability to greatly enhance a clone's learning abilities. Perhaps by spending a significant amount of some expensive ingredient (probably luciferium for flavor purposes?) and extra 10~ days of cloning time, the resulting clone would receive an interested / burning passion buff for all skills and a modest, permanent learning buff. I don't know how that would play along with brainwave scanning (if at all - a key tradeoff for balance's sake maybe).

Perhaps instead of learning, an enhanced clone would be exceptionally durable, naturally immune to any disease, or any number of other things as QE devs see fit.