I thought it just impossible how he could have survived being completely disintegrated (almost Palpatine/Megatron style) to have anything left of him to make into a robot in the mid credits scene.
Well, I have a possible explanation.
What if, Nefarious didn't survive, but he had previously programmed his machines to, in the event of his death, make a robot version of him, programmed to think he was the original Nefarious with his memory, personality, etc. (perhaps a different personality if you think it and the games are the same continuity), to continue his reign of terror?
It seems the repairbots discovered him in the wreckage, but perhaps Nefarious had already built and programmed his robot clone, either awakened somehow from the crash, or designed to awaken when the original Nefarious's life force was gone. (He did seem to be in a small chamber as if it was a chamber his robot body was being kept in)
Means of course Ratchet will still have the robot Nefarious to fight, but I can headcanon in an unseen battle not documented in a nonexistent sequel, he will eventually defeat him (that or the games), and the awesome disintegration can still stand.