I've had this thought before, and it does make a lot of thematic sense -- my only possible niggle is that all that juicy hydra poison will be completely ineffective against the Ashen Empire.
You could always reverse it and do a (magic-nerfed) classic Pythium in the late age, and the Serpent Cult in the middle age. You could explain this by changing the backstory: instead of Pythium being the Ermorian province that was once Sauromatia, make it Sauromatia that had been changed by waves of Ermorian refugees. In the late age, the Ermorian/Pythian culture would now be dominant, with a correspondingly reduced emphasis on hydras.