Well all the Gods are kept in some kind of mystery so that no one really knows their true origins but people like to make up theories on it and the most reasonable theories get the go ahead but the other ideas on how they came to be also remain as the less popular choice or choices. GW isn't going to just say Khorne came from this while all Eldar Gods are these and the Emperor is from this they I assume like to keep the mystery about it so that people can make up theories just like people do with the II and XI Legions, then drop a hint and nudge here and there just to get people thinking about it.
Are the C'tan similar to chaos gods/major daemon entities, or are they their own seperate deal altogether.
Separate, they are some sorta entities that feed of various sources and eventually found souls to be tasty. They are moving, intelligent black holes that hunger.
One of the theories for what will happen in the 40k end times (maybe 10-20 years from now or something) is that when shit hits the fan and the golden throne fails/gets destroyed, The Emperor is going to be reborn in the warp as a new chaos god. With the Imperium powering him far more than any individual chaos god, he's going to proceed to beat the shit out of everything else in there.
Actually, there is a theory that if they were to let the emperor die, at this point he would become the God of Order, and either defeat or slow the Chaos Gods- Much like Sigmar in the new warhammer fantasy stories.
The Eldar are the most warp sensitive race in the galaxy as well as their capacity for emotion(i.e how passionate they can become) far exceeds normal humans and thus their resonate far more strongly in the Warp. So it essentially took an entire race of pyskers, at the height of their galaxy-spanning empire, to become so enslaved to hedonism and excess that the echoes of this unparalleled debauchery gave birth to a sentience that was the sum of their collective sins. And then untold billions of Eldar souls being violently ripped from their flesh and thrown into the warp to feed the new Prince of Chaos so he could grow big and strong. So if souls are the currency of the Warp, then your average Eldar is worth 10x as much as your average human, and making a new god aint cheap. The only other exception to this are Orks(and perhaps in a strange way Tyranids) who, though incredibly simple minded, can collectively bend the laws of reality via the power of WAAAAGH. The more Orks gathered together, the stronger the WAAAGH gets, so at some point it's very likely that there were enough Orks(probably when the Old Ones first made them to fight Crons) to actually make Gork and Mork manifest in the Warp. At the very least their belief in their gods is just as powerful as their belief in certain colors altering the properties of objects. Humans born with the psyker-gene are exceedingly rare(though with trillions of humans, 1 in 10k doesn't seem so low) and among those there are fewer still who show any real potential of significant power. The majority of these are sent to Terra where the Astronomican drains them of their soul-essence to sustain the Emperor on the Golden Throne. So, like the Chaos gods, the Emperor basically feeds on souls. Albeit in a far more benign and preferable way, you still become part of the gestalt entity of countless souls that is the Immortal Emperor. The only way for a "new" chaos god to be created without an extinction level of soul sacrifice is Ahriman finding the Black Library.
I believe humanity already created a new during or shortly after the great crusade, the decree of the emperor to banish religion generated much stigma and atheism towards the existing beliefs commonly associated with all races, anger, decay, pleasure and... fate etc. Keeping with that rule that emotions manifest in the warp, it should also be true to that of the unbelief during the unification wars up until the horus heresy, when ALL of humanity (and that's billions and billions of minds) was led to believe that there were no gods. This is rumored to have birthed the chaos god Malice (with it's follower legion "The sons of malice"), a god dedicated to the eradication of belief and a pantheon of atheism. Contrary to this, after the fall of the Emperor and his internment on the golden throne, humanity as a whole started to place faith in him as a god, ironically, diminishing Malices power considerably and why we would not see it come to fruition as slaanesh did with the Eldar fall. This could have been the ploy by the Emperor from the start, to eliminate religion and birth a god (unknown to humanity) dedicated to the eradication of belief, and with it the chaos gods themselves.
