Ok I don't know if this is possible from programming/mechanics point of view and would it mess up the whole game, but I would do "Classic Mode" something like this:
1. Just one age, with all the tech trees put together. No era changes or crises, just one long era from antique to modern.
2. Choose any civ at the start you like. Also ai civs can be anything.
Some civs like Rome would have their unique units in early part of the game, some like Prussia a bit more spread out (Hussars in "late renaissance"/industrial part of the age, Stuka planes in the later stage).
3. Some civs' unique ability would need to be rewritten, for example French Empire "You can select the Celebration effects of any Government in the Modern Age. " would need to be changed.
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It's not perfect, but it would put civ switching and three ages to rest.
There still would be plenty of content to play with, like commanders, navigable rivers, new diplomacy(that I love!), towns vs cities etc.
I would probably reinstall the game.
It would allow empires to progress in their own pace, we would get again wars with huge technological differences and we could do the sandbox-style fun games.