AFAIK (and someone go ahead and correct me!) there aren't any simulations that go both as broad (in terms of features) and as deep (in terms of what those features do) as that.
Something like Civilization or Europa Universalis will offer you an 'epic scale' sim of how a nation can grow and change over eons, something like Patrician or Anno will let you tinker with economic models, something like railroad tycoon or cities in motion will let you dive deep into infrastructure and transport models, something like Tropico will let you dabble with edicts and laws and their effects on a population...
Basically, if you figure out what system(s) you are most interested in, you'll be able to find something that will delve deep enough to scratch an itch, or go for something shallower that contains a lot more systems at a much bigger level (and nobody is going to accuse a Europa Universalis of being 'shallow' even if it does not model individual cities, or let you get hands on with its economy)