They never call him "the Fallen," he's never shown to be evil, is a victim of Sentinel's betrayal like the rest of them, and his force ghost is there to approve of Orion getting the Matrix.Did they decide that?
All I remember is that he was this mythical figure of great power that D-16 looked up to. I don't recall anything to indicate that there wasn't more... than meets the eye.
They don't really give any of the Thirteen deep characterization outside of Alpha Trion, but it seems like they were eschewing the whole "Megatronus goes bad" plot. Instead they make him a pretty strong warrior of legend who D-16 idolizes for all the wrong reasons.