Formation Level Capabilities, rather than Element Level Capabilities
What if instead of having capabilities be applied to an element, they could be applied to the formation instead? For instance, say I create a regular infantry battalion with no additional capabilities. Then, I could duplicate the formation and give the entire new formation template extreme temperature capabilities. For capabilities like genetic enhancements, it would apply exclusively to the infantry in the formation, of course.
For non-capability elements that get added to such a formation after construction, the incoming units could have their morale set to 0 and you pay the difference in wealth cost between the non-capability element and the with-capability version of the element, abstracted as the incoming element is "undergoing retraining/refits/enhancements" as they are being implemented into the new unit. That way, you couldn't cheese your way into getting elements with capabilities by simply dragging them into a formation with a capability.
Theoretically, you wouldn't even have to create a new formation to do this. When selecting a formation on the ground units screen, there could be a button to change the formation's capabilities, in which case the rule in the previous paragraph would take place and apply to the units already in the formation.
So for instance, let's say I have an infantry formation that already has desert warfare capabilities, but I also want it to have extreme temperature capabilities. I select the battalion, click "Modify Capabilities", and select extreme temperature in addition to desert warfare. The formation's elements' moral goes to 0, I pay the additional wealth cost, and the formation now has the capability (with the units within not being combat effective in the slightest due to the 0 moral.) Eventually, their moral ticks back up to normal levels. If I were to drag a vehicle into a solely infantry battalion with genetic enhancement, I would think the game could easily recognize the incoming formation is a vehicle, and thus not do anything. The vehicle's moral would not be affected and no additional cost would be incurred, seeing as vehicles can not receive genetic enhancement.
Reduced Missile Radiation Research Line
We can research enhanced missile radiation if we want to glass planets, but what if we could research reduced missile radiation for tactical ballistic missiles for use in assisting ground forces without ruining the planet?