Give an upgrate to only one unit
I suggest the "come-back" of the système that was used in C&C:General:
I mean the ability to give an upgrade to only one unit.
For example, a main GDI tank witch can be upgraded with
-advanced munition (make it able to switch between anti-tank and anti-infantry shells, efficient against infantry and light and medium vehicles)
-a rail-gun : less efficient vs infantry than the other upgrade, but really dangerous for all vehicles.
Allow advanced strategy and oblige the player to chose specifics upgrade depending of his strategy or the enemy's strategy.
This oblige the player to make micro-management because if you unlock a weapon biotechnology, it do not mean that your tank will use it, you need to upgrade each one separately.
Impossible to find a media about it, so, I just give you some examples from General :
-most american vehicles (it was drone, but it had the same effect)
-Overlord Tank : bunker(allow garrison of 5 soldiers), propaganda tower(boost your allied), Gatling(secondary weapon effective against aircraft and infantry)