Eh . . . I think that would end up as a mess, unfortunately, trying to balance units from different eras.
Yeah, it's kept Civ from getting any traction in the market
I have a different take, and think that balance is not a thing we should aim for in wargaming , aside perhaps from considerations for multiplayer matches. I've written long posts over at Combat Mission's boards about this, how seeking 'balance' is misguided when designing war games and scenarios. I think asymmetry is a desirable thing. Clashes between two matched forces have their appeal, but more interesting to me is finding success when things are not on an even footing. History of course is filled with dissimilar forces joining battle.
How to beat cannons with your archers. Or armor with your cav. I don't see lack of balance as a disqualifier, but a challenge to overcome. Of course, sometimes I'm the one with the guided missiles.
I think it would work splendidly in Total War. Let's say you have three pillars of your empire, and call them Military, Economic and Technology. The balance is in how the player prioritizes each. An Eras game would allow the player to seek his own balance between these competing things, and if he allows his Military to lag, by choice or by circumstance, it's just a consequence of decisions, actions or circumstances, some perhaps out of his control.
There would be no attempt for the designers to balance units from different eras, that seems impossible. Parity or ascendance is sought through the game play, and not baked in by the design decisions. Or that's how I would see it.