The Creators (humans) went extinct somewhere in the past.If we take into account the galaxy-busting Wave Motion Gun, the mere existence of such a weapon could have raised a giant red flag of biblical proportions and The Net could have warned their human masters about the existence of a potentially deadly weapon who, not only could destroy all the living beings in the space and derailing centuries worth of experimental research, but also put the entire human race in danger as well. Since it didn't happened yet so far, it's because of two potentially possible scenarios:
- The humans went extinct somewhere in the past, so The Net doesn't have anyone to report or answer to. Considering all the manipulations all the sides of the conflict did on The Net, it's very possible the Logic Bomb The Net suffered later in the story was aggravated due to the conflicting orders regarding protecting all the Species from self-induced harm. Oddly enough, in Birthright the same plot point was brought back again, except this time it seems The Net or the remainings of it is doing something about it, as it's implied The Net sent a message torpedo towards somewhere in the space. Why The Net decided to wait two centuries to possibly warn their masters, when it could did that when the ILR-EDF war was still raging is an unknown mystery to this date.
- The Earth is too far away from the setting of the whole anthropomorphic civilization, possibly even in a different galaxy, meaning that, even if an apocalytic scenario happens, the Earth will not be affected at all, other than the liability of losing millions of lives worth of scientific experiments.
- This theory was Jossed by Word of God in the second Story Arc as it seems the humanity still exists and not only they're completely aware about what's going on, but also they seems to deployed some kind of protocols to prevent both the anthropomorphics and humans themselves to be mutually destroyed while still keeping the things controlled from far away.
The Creators are/were NERV.During some point during the conflict against the Angels, NERV (and by default, Gendo Ikari and possibly Ritsuko Akagi) designed a backup plan in the case the Angels managed to reach their objetive to reach Adam and causing the Third Impact and the extinction of mankind. That plan involves genetically modify Earth animals and send them to the space in another solar system, so in the case the human race were exterminated by the Angels or by the Third Impact, those modified, humanized animals can fight back against the Angels, assuming the can be able to find the Evangelions (and also find the right pilots to pilot them). Taking into account what happens in The End of Evangelion, it will not very hard at least to find the EVA-01 floating somewhere in the space, and since this is NERV we're talking about, an organization able to build giant organic humanoids build to fight the Angels, creating anthropomorphic animals could be a piece of cake for them.
In any case, if the Angels appears in the middle of the ILR-EDF war, all the sides of the conflict (including Enchawah Corp.) will possibly has to choose between finding the way how to stop the Angels, unless they find at least the derelict EVA-01 or joining forces to stop them, unless they want to be destroyed by them.
NOTE: This is still applicable towards the Rebuild of Evangelion films, assuming the newer films ends in a similar way The End of Evangelion ended.
The Creators are the other EDF/Cosmo Force
Just like in the Evangelion case, the human members of the Yamato's EDF used genetic engineering to create humanized animals just in the case the whole human race got wiped out if the Yamato didn't return from Iscandar for saving the Earth, so the Species should avenge their spiritual homeland against the Gamilas Empire or whatever race responsable of the destruction of the human race. It's very possible the derelict human ship is possibly a Yamato-class or a similar class, because it's the only way how the Albedo's EDF managed to get their hands on the technology for creating their own Wave Motion Gun, except that weapon is possiby an upgraded/experimental version of the original one used by the Yamato, created specifically for destroying solar systems in a single shot. After reverse engineering the Yamato-class WMG, they raised the power of the weapon to be able to destroy whole galaxies with it.
The only side-effect of all this is since the Albedo's EDF tested the WMG against a ILR fleet in the second arc, that means, or the Yamato's EDF and by default the very original Yamato will have to sortie to find out what happened there, meaning Captain Okita, Kodai and the rest of the crew will have to stop the Albedo's EDF and very possibly against the ILR as well, ignoring the Awful Truth behind the creation of the Species in an attempt of their own EDF to destroy the truth, thinking they're fighting against just another alien race and possibly they had to face against Erma Felna along the way. And let's not forget the Gamilas Empire as well, making the whole thing into a giant galactic Mêlée à Trois between too many antagonic forces.
The Talents are another name for Puella Magi and The Net's real identity is Kyubey.
The story are more or less the same as canon, but with a twist: The whole setting is a product of one of Homura Akemi's universal resets and Kyubey and the rest of the Incubators are manipulating the Talents like Erma so they can harvest more energy from them, with the additional privilege Homura cannot stop them this time because she doesn't know the whole existence of the whole anthropomorphic civilization, so even in the case she stopped both Madoka and Kyubey, he could find other idiots who can give that energy.