Was Re:Creators originally planned to feature fictional works that actually exist in the real world?
As cool as it sounds, I find it highly improbable. Someone might have gotten the idea at the start of the production, but simple thought about it makes it extremely difficult to pull off.

The major hurdle is licensing. Getting licenses to all the shows and characters would be massive undertaking and would take massive amounts of time, effort and money.

Next is getting authors of other works agree to have someone else write official story with their own characters. I'm sure most authors would not be fine having their own characters being written by someone else.

There is also a problem of fitting the characters into the story. Many popular characters have clearly defined personality and fitting that personality into the story might not be easy. And while many characters are clearly influenced or based on other fictional characters, there are none who would fit into the story exactly.

Another thing is fan perception. If characters from existing stories would be used, it would change canon as seen by fans. And it is not something authors of the originals might want. And it might take some twisting of the character's personalities to fit them into the story, resulting in outrage of fans at clearly out-of-character depiction of their favorites.

So no, I don't think this was ever a worthy idea during production of Re:Creators.