For the Athenians, can't you divide eras through an upgrade in the prytaneion or by initial choice? For the latter, You can decide whether to take either the Greco-Persian or the Peloponnesian hero roster at the beginning of a match.
Or way better... choose from one of three/four ages: Greco-Persian, Pelopponesian, Hellenistic (, or Roman); then one of four heroes of the selected era. This opens up more heroes to choose from, notably Cassander.