There are a few ideas on the hiarchie. After all.. most theories stay or fall with Nihilanths role.. and thats the most unclear one.
(I forgot the garg.. I'll add lateron. sry)

Nihilanth is God
Ah.. theory one where he is on top. :) I aint putting wildlife in simply cause they are just wildlife.. its basiclyly crab is below.. others are predators.. end. lol. :)

In this theory the hiarchie is
Nihilanth
Controllers
Slaves
Agrunts

This cause the alien grunt is breed and has no brains. Not wise to give it status. :)

In here the great Nihilanth was hurt in a accident / war of unknown reasons. Hence the enormous damage to his body. To keep him from further problems he lives in a chamber deep in Xen. (where he was finally tracked down by freeman) The fact that he's maimed might be cause there were no healing pools available cause of the accident/war.. As a great leader he let his race use the pools while he was forced to "heal" by normal surgury.

The controllers, children of Nihilanth (but another race) are the second in command.. Since nihilanth is the only one of his race who survived the accident/war they have taken over most duties of the great god. Maybe thats why they were created in the first place.. To help Nihilanth now he's down. There large numbers and basic duplication of nihilanth powers help them in there cause.

Slaves.. they do the basic work.. probably created after the controllers (maybe cause Nihilanth found out they had limits his race didn't) they are ment to do work. They got brainpower to succeed in extreme difficult tasks and also have the muccle to do those tasks. Since they are so strong and intelligent they were collars, probably to let them being controlled.. They can be chained up by the ones on the neck and wrists. Its lickely that in time they got more status after good work and no rebellion. Humans atleast haven't seen them chained up. And they are left without controllers to check on em multiple times.

Alien Grunts. they are breed and they got little brainpower. they relay more on pure strength. Its certain that the Slaves have way more intelligence then alien grunts. Also by the fact that those soldiers are just put into battle to die while slaves are mostly kept safe on Xen to work. Some slaves have been seen on Earth but since, even on Xen, the numbers of controllers seem small its likely that they are send to command these grunts.

Nihilanth.. Enslaved god
Another VERY reasonable theory is this one. It is very seemingly that Nihilanth is kept against his wish in the chamber in Xen.. His race probably was with many. Then one reason or another they got in a fight, probably against (fellow) Xonians.. (the big question in this is if nihilanth is a Xonian). Overpowered by Xonian forces his race was destroyed and him being captured.. The lack of large numbers of gargantuas, Xonian Ships and gonarchs probably shows the force needed to acomplish this huge task.

Maimed to strip him of most of his energy (and thereby power) forced him to work for the Xonians, do as they wish. The controllers, probably needing him to have special skills (more?), attached a extra arm to his body by surgery.. (non Xonian) If he is Xonian that arm was probably blown of without the Xonians capable/wanting to use a healing pool... so just stiching it on.

This makes the NEW hiarchie
Nihilanth
Controllers
Slaves
AGrunts
Nihilanth

Nihilanth is in 2 timed cause he is below as a prisoner but again on top cause he (forced though) takes care of anything.

Nothing else changes expet for the part that Xonians watch there back on theory 2.
I myself prefer theory one, as the war part, cause after all... Who would keep that kind of thing living? :D