I'm in agreement that I can definitely see Varis aiding the Scions and forging a sort of temporary alliance to defeat the Ascians. He claimed he had a desire to 'bring the reins of history back to humanity' or something like that after all. Between that and his outright disgust towards Solus he's implied to very much not be a fan of them and their manipulations. However...I don't honestly see him becoming a 'good guy'. He's still the leader of a genocidal evil empire, and he was seemingly with (possibly leading) the Optimate faction that sees the Garlean Empire as superior. He fought against his uncle, who wanted to cool the imperialistic ambitions and aim for friendlier foreign policy. Him being against the Ascians and against Eorzea are not mutually exclusive concepts. I would not be shocked if after dealing with the Ascian question he might then turn right back to the conquering. With characters like Fordola and seemingly Gaius heading towards opposing Garlemald and becoming better people, it would make sense if he took a very different stand on Garlemald. One guess is that he could end up something like Vayne from FFXII, who had noble aims but was still a villain in the end.

That being said, he's still something of a wild card. I don't know when or if he'll die, nor do I know exactly where he'll land in the grand scheme of things. He's definitely important, they wouldn't have given him the big reveal scene of the last patch or a prominent place in the 4.5 trailer if he wasn't. But other than that I can't be totally sure. I do have to admit they've piqued my interest in a character I had previously written off as boring though.