Wow, these changes would make for a very interesting game.
As for minos, about how many come in at a time in the early game? Sorry, but I don't have the beta.
If the number could be increased as well as their strength and damage and stuff being increased (initially I mean, not after getting a certain flag) it would make for an interesting change.
And forgive me if there is already a flag like this, but how about having a building that actually causes your enemies minos to decrease in number? Half the time you wouldn't want it because you need XP, but it would become really useful lategame.
A name like Ennui of Amaterasu (Japanese sun god), maybe.
And as Col Jessep suggested, perhaps buildings that when captured cause weather changes (to your advantage). Such as random periods of snow, or rain, or sandstorms (maybe 1 - 2 minutes) that slow down, reduce damage, etc your opponents more than you. Or perhaps even random meteor showers, or earthquakes?