The issue that bugs me most is how Heros, Henchmen, and even Spirits affect Minions. Heros and Henchmen seem to waste energy and skills healing Minions, when most of the time we want them to die, in order to trigger Death Nova or Jagged Bones. A Rts defensive Spirits die almost immediatly if you have a Minion army. I dont like that.

I suggest handing full control of Minions to Necromancers only. Make it so only Necromancers can be the only ally that can influence Minions. I'm not sure how intensive it would be to change this, but one way might be by changing their ally status. If Minions where given a special ally status that may fix this issue. Keep in mind, skills like "Go for the Eyes!" or "Fall Back!" may or may not trigger after these changes.
The other work around might be changing how H/H and Spirits affect just minions. That may require modifing H/H AI and Spirit mechanics. Regardless of how it gets done, the goal is to reduce H/H and Spirit waste on Minions