Suggestion:- The ability to do more scientific projects throughout the ages, like the time machine, I guess you could expand on that with more story to it maybe? Also the ability to see population graph, happiness graphs, so you can see your progress throughout the ages, You should also have a map mode, expand your empire on land and beyond... infinite maps to conquer , so basically a monarchy civlization simulator, so even after the story has finished, you can still mess about . Perhaps more yes or no questions, to do with science , technology upgrades and perhaps issuing decrees ,say yes or no to a proposal for a decree, which can have a positive or negative effects on your stats?
just a thought