I'd like to see Civs remain the constant through the ages while our Leaders change. If the goal here is to build a Civilization to stand the test of time, then at least give us the opportunity to remain "America" if we choose to play as them in the Antiquity era. In other words, each Civilization would have three pools of Leaders. One set for Antiquity, one set for Exploration and one set for Modern. Would be a rather difficult task for some Civilizations while others, like America, would be rather easy. In America's case, as an example, Antiquity Era would be any one of the Founding Fathers: Washington, Adams(John or Samuel), Jefferson, Madison(wouldn't mind him honestly given 1812) or Monroe(ditto w/ Monroe Doctrine). When moving onto the Exploration Era, Andrew Jackson would be an easy pick given all the Exploration Expeditions while he was President(although one could argue John Quincy Adams deserves the credit). Then in Modern era, you have quite a few: Teddy(Great White Fleet), FDR(WW2), Eisenhower, JFK, etc.
Leaders and their skill trees could be reset for each era(leveling the playing field). I mean I understand the notion of Civ's evolving over time, but we risk destroying tradition in Civ as I see it.