It is definitely the one in A Crack In Time. As others have said, turning everyone in one galaxy into robots (I realize he may have planed to move to others to do the same)is nothing compared to having the antagonists throughout history always win, or worse, disrupting the balance of time and the universe, which is actually a very BIG deal for a Ratchet and Clank game. But whether Nefarious got his desired result from tampering with the clock or not it would have been chaotic either way.
if the clock worked like that it would make for a line up of pretty awesome games! Fixing all the damage Nefarious is causing. Could keep the series going a little longer (a bit more than FOREVER!
)
Do explain.
Let's say Nefarious went back and found say… Captain Darkstar! He teams up with old Darkstar and helps him with his Qwark problems, so it's up to Ratchet, Clank and Qwark (who doesn't know R&C) to stop Darkstar! That should make for a game on it's own, then another involving Drek, maybe Nefarious could take Qwark's place, but this would mean Qwark becomes forgotten. So Ratchet teams up with Qwark to stop Nefarious and Drek.
After stopping Drek (or maybe failing to stop Drek) Qwark gets no fame and fortune, and is lost forever. This becomes a problem for Ratchet and Clank (knowing what happened last time), so they head to Bogon and search for Qwark, maybe finding that Nefarious had teamed up with the Thugs, they may fail to stop the Thugs, or succeed. And then head back to Solana to find Qwark has gotten his reputation back (maybe he finished of Drek or some other bad guy, depending on what happens to Drek in the end of the first one)
Then Nefarious teams up with Vox industries, and spreads across the whole of Solana, making a show for the entire Universe to see, heroes and villains battling it out for the Galaxy! Then Ratchet puts a stop to this once and for all (by stopping Vox and Nefarious and the other villains hired by Vox and Nefarious. (lets shove Slag and Tachyon in there) and it all ends right where we were at the end of ACiT 
I just came up with that on the spot, and obviously limiting myself to the villains introduced by Insomniac Games. So imagine what Insomniac could do with the idea! With all new villains they could introduce in the past, and maybe going back even before Darkstar! The possibilities are endless. Sure the possibilities are endless with the end of ACiT the way it was, but this way could have been exciting still.
And many fans might be happy that Qwark gets completely re-made
(not looking like a complete A-hole this time)