My theory is that Nihilant and the controllers are the same race, and that the controllers are widely related with the Vortigaunts. Both are intelligent races that have a collective mental telepathic conection (or whatever you wanna call it) between their own species and both lived in the same planet. The Combine came to that planet (not Xen, remeber that nothing is native from Xen) to conquer those races, but they fled to Xen, however, in the end, the combine conquered them. They controlled one of the Controllers (Nihilant), modifying his body, putting him in a “slave machine” and locking him in a room from wich he can’t scape to control the rest of the controllers, whom at the same control the Vortigaunts by the bracelets you see on them (remember that near a group of Vortigaunts there’s allways a controller in Xen).
That means a chain of mental control:
Combine----->Nihilant----->Controllers----->Vorts :fffuuu:
The Alien Grunts are just like the Overwatch Soldiers on earth: heavily genetically modified Vortigaunts with “brainwashed minds” and deleted memories, and because of that is not necesary to control them, the same way is not necesary to repress violently and put great amounts of propaganda on the Overwatch Soldiers on earth. The main combat force of the Combine Xenian Army are the Grunts, the Vortigaunts are just used as slaves that work at the factories creating grunts, and are not intended to be a combat force, but since pretty much all Xenian living forms were teleported to earth, and the slave Vortigaunts take a defensive and violent approach against “intruders” they started to attack everyone in Black Mesa, just like all the Xenian beings