Baelsar always did meet his full potential as a character in that uncomfortable gray area between friend and foe. Even when he conspired against Nael van Darnus you knew damn well he had no love for Eorzeans; they remained willfully ignorant, put their faith in false gods, trusted their nations to those with no right to lead, and refused to embrace a strong, structured order.
I also agree that the Griffin's collusion with Elidibus is hefty evidence against the Gaius theory. Plainly, the guy should know better. That's actually part of what drives me nuts about the final scenes, though. When the Griffin speaks to Elidibus, he compares their leadership, pointing out that he has provided the Ala Mhigan Resistance with tangible benefits while (correctly) assuming that the Warriors of Darkness ("your pawns") got nothing of value from him, in the end. He plainly doesn't like or trust Elidibus, as if he has some experience with how Ascian machinations work.
I need to study this patch a bit closer before I comment too much on any of it.
My understanding is still rather vague, the evidence fits from even opposite angles. <furrows brow>