I think, scenarios are a good possibility to design fictional and/or fantastic situations, but for historical ones, they're too inaccurate. I also think that the limited timespan for a scenario is a true handicap.

Let's make it clear: I'd prefer a combination of scenarios and new games...
When you start a new game, you'd be asked about the era you want to star in. Then, for every preparated era, there could be premade entire worlds, with premade empire borders, science and military stuff (like in scenarios). Now, you wouldn't have to choose one of seven (or similar) simultaneous existing cultures but one of ALL given civilizations existing in the game. The other realms and civilizations would be played by AI, as usual....
So the whole game would be de facto ONE scenario, it wouldn't be necessary to create additional historical scenarios, because they would be included in a standard game.
Surely, you'd have the opportunity to create fictional/fantastic scenarios or scenarios that base on a different way of history.
There could also be the possibility to change the worlds that are given for the special era or epoch.

EXAMPLE:
1. New Game On Earth/Europe (not really important now)
2. Game In Modern Times
3. Year: 1796
4. Civ: Prussians/Germans

So one would start with Prussia in 1796, surrounded by other great powers and minor nations (like Austria, France, Russia and zerland and the Netherlands). There should also be as many civs as possible in the world. For this example, the world map should be a BIG one, to really make sense of the reign over a European power like Prussia (which would consist of e.g. Berlin, Danzig, Stettin, Königsberg, Warsaw, Breslau etc.). Yes, this method should also work with 1941, 800BC, 1096 and any year you wnat to start in. (might become awful to create every empire for every posible turn (or maybe every era), but that's not our problem.
Whether an empire should only consist of cities or also have borders (I'm for borders) is to be cleared in other discussions.