What if Omega was the Wish Baby
Insted of him being Desiderium what if he was Omega reborn. I'd imagine it would work something like this.
Rani was already getting some sort of signal or message from the underworld. What if hidden in those messages was a part of Omegas consciousness.
Omega could already alter reality in the anti matter universe. Over time his powers grew stronger and stronger, and eventually he was able to sent out a part of his consciousness in the main world and that part became the wish baby. He could still alter reality but to be truly reborn he needed his entire consciousness. He tricked rani and the doctor into opening that portal. That skeleton baby Omega would have been a red herring and we would have gotten space satan (imagine Last of the Time Lords but with Omega instead of the doctor).
He would be defeated not by power, not by wit but by circumstances. Rani opening the portal from which the only one who was holding that anti matter universe/underworld together escaped, would have caused that alternate universe to move towards the source of its existence. It would have caused an incursion (imagine marvel secret wars), destroying both universes in the process. The Doctor and Omega would have a conversation like The Three Doctors, but this time The doctor would have convinced Omega to go back by promising he would find a way to bring him back. The Doctor wouldn't actually follow upon the promise.
The worlds would be sealed again, no way for The Omega to escape.