You people are so boooring! Seriously? You're against the very idea of an ultimate strategy game? Sad is all I can say.
I'm all in favour of such a game. Quite an easy way to handle it too. Let's Paradox announces Historia Universalis. An epic game spanning from 500BC to 2000 AD. And then they release the following games. Or rather, one game and four very big add-ons.
1. Historia Universalis : The Dawn of Civilisation - 500 BC to, let's say the start of the Dark Ages.
2. Historia Universalis : The Dark Ages - The medevial times.
3. Historia Universalis : The Rennesaince - From the end of the medevial times to the start of the Industrial era.
4. Historia Universalis : Empires - Industrial era.
5. Historia Universalis : The Dusk of Civilisation - The modern age.
All those games would have the same core. Technological trees, warfare, population and all that. And with each game the available units and techs would change while the mechanics stayed the same. In the first part, pops would be scholars, slaves, soldiers, etc. and in, say, the third we would have artists and such.
The mechanics would stay the same while the player would be able to experience the industrial boom as well as the introduction of feudalism. Another thing would be various transfer dates. If you developed the necesarry technologies in 100 BC, then you would go to the Dark Ages in 100 BC.
As a way of stopping complete domination of the world, the player would be able to take control of any nation that sprang up in the world by a pop up. You're playing Rome and the Goths have just become a Horde. In the pop up you can decide to take control of the Goths and lead them in their quest to destroy the Roman Empire. If the player would decide to stay the same nation all the time, he would find the game getting harder and harder with each century. If you would want to keep the whole Roman Empire together, you'd be getting crippling penalties in the Dark Ages, and if you continued into the Rennesaince, you'd be pretty much in a state of constant revolt as no-one would be listening to your rule and everyone would be attacking you. Of course, if you were a colonial empire that developed in the "Empires" you would face little problems in the early "DoC" but in the later parts of it, you'd be getting severe penalties in the colonies, leading to de-colonialism.
I could go on and on but I'm lazy by nature and don't feel like continuing.

And if you ask "What's the difference with the original Europa Universalis series?", my answer is "The same core leading to conversions with no problems whatsoever and with the possibility to build the Frankish Empire on the ruins of the Seleucid Empire in the Balkans, and fight off the catholic norse while upholding the values of the Great Sun God in your quest to develop rockets with which you shall colonise Mars in the year of our lord 1864."