why not simply tweak minions to scale as your damage, health and mana get larger?
if a general's minions had a certain percentage of their demigod's life and damage, then they scale as the demigod does, and as they get items.
this way, no skill tree is really invalidated, and if a few of the skills seem weak, you can change the skills that grant +health and +damage to minions to percentages as well. ie: the queen's entourage skill - instead of +200 life and +10 damage, maybe +20% life and +5% damage. keep in mind these are just example values.
this way there is more incentive for the minions to be used in conjunction with the demigod, rather than just another skill. Whenever possible, skills involving the minions should probably also affect the demigod as well.
if it grants your shamblers more life, maybe it reduces the cost of summoning them too? or there is a life regen bonus for the Demigod while the minions are alive.
Remember, it should be about synergy between the minions and their General, not having to choose one or the other to be effective.
In my opinon, every skill a general has should affect their minions, so while you customize your demigod, you also customize the minons you have. To continue with the Queen of thorns example, if you put points in Spike wave, your shamblers attacks reduce move speed. add points to uproot? minions do more damage to structures. spike wave? minions get a damage bonus. bramble shield? minino life boost.. or each time bramble shield is cast, you heal your minions for a bit.
be creative! someone come up with something similar for the other generals!