Back in the Yamato 2202 thread, I commented that the biggest waste of storyline was not having Knox (sorry I can't think of his Japanese name) be the traitor who shuts down the Wave Motion engine when the Yamato is confronting Gatlantis at Saturn.
The writers had already established that Knox was a clone of the real Knox and that, thanks to a telepathic link to Gatlantis and Zodar, that could have been used to "activate" Knox and have him disable the engine and frame Conroy in the process, thus giving both men reason for actions later in the series.
They did establish that Saito (Knox) was a brainwashed Gatlantis agent without his knowledge, that he provided some vital intelligence or something. As for Kato (Conroy), I think it was more powerful that he wasn't framed, but was manipulated into doing it to save his son.
Although I didn't get the logic of Zwordar's whole "People of Earth, I give you the gift of a cure for your children, before I destroy the entire human race in a few hours."
As for the Time Fault, I don't entirely remember the original season 2, but my impression was that the Time Fault was something the remake invented to rationalize the implausibly rapid fleet rebuilding in the original. And once they had the idea, they used it as a source of complications and moral questions.