Honestly at this point the line should probably just pony up and start calling the Shogunate the Second Age - which might remind more people that it, you know, existed - and the current Age the Third.
(Actually if you're measuring objectively we're probably on the Fourth or Fifth right now, with either Zen Mu or Primordial-ruled Creation being the first depending on whether you're counting from the waking of the Primordials as the first thing distinguished from formless chaos [1] or the establishment of linear time as, you know, the point you can started measuring "Ages", but the Exalted Host of the First Age were strangely reluctant to write those parts into the history books.)
[1] Raksha don't get to count as an Age of their own.
How about this? Every time there's a crisis severe enough that the calendar needs to be reset, it's a new Age. Every Age has an Ascending phase where somebody conquers or otherwise firmly unites Creation, a Resplendent phase where wonders are built within that societal framework, a crisis where flaws present at the foundation (and slowly escalating ever since) finally explode, a Descending phase where unity progressively breaks down, and finally a cataclysm which could have been prevented if only coordinated action on the appropriate scale were still possible.
Zeroth Age
Ascending: Theion challengers Mardukth for leadership of the tribe of dreamers
Resplendent: Time of Glory
Crisis: incarnae try to unionize
Descending: Primordial War
creation of Underworld and Demon Realm
First Age
Ascending: Exalted Host subjugate everything they can find
Resplendent: industrial mass-production of artifacts
Crisis: Facet Raven dies of old age
Descending: Thousand Struggles Era
Time of Cascading Years
Second Age
Ascending: Deliberative re-founded, fundamental forces examined
Resplendent: industrial mass-production of abstract concepts
Crisis: Great Prophecy, Usurpation
Descending: Shogunate
Balorian Crusade and Great Contagion
Third Age
Ascending: Scarlet Empress owns the Blessed Isle
Resplendent: Dynasts and Immaculates leave their marks on the rest
Crisis: Jade Prison breaks, Big Red vanishes
Descending: default "time of tumult" setting, consult your GM for further details
Cataclysm: whichever of the Thousand Dooms the PCs forgot until it was too late (far too late for now, anyway)
Then the long game is ultimately about determining the shape of the Fourth Age.