There definitely needs to be more work end-game. Heck, even the basic city-management basically stops at airports.
Really I think what needs to happen is that the game progresses in 2 stages - the current game is pretty awesome up to about the industrial revolution. But after that, there's a whole lot more that we should do:
-The "old" districts basically need to be retired at that point. Seriously, there is no city at the scale that we're talking about in civ that doesn't have a market, library, etc... by this time. We can't just give every city a free campus/library, but would be nice to transition new cities to maybe a simple model where they spend X on "public infrastructure" and get multiple bonuses
-We should be forced to specialize industries in our cities more. I think someone proposed a model for factories where they would basically take raw goods and produce different finished goods (ie. a factory that has dyes and silk in its region may produce a new luxury, printed textiles)
-We should be forced to manually remake the land. That old mine that's now 5000 years old? Maybe we need an upgrade to it. Could be instead of getting the free extra cog from it, there's a new "modern mine" or something with different bonuses. This could also help us manually reshape the land to the modern era
-There should be more focus on new buildings. If we're forced to build libraries and markets, why don't we have the modern supermarket, movie theatre, aquarium, public transit, recycling centres, etc...
-With this, in the modern times we also need to be more concerned with the environment as well. Or maybe you also can run government-types that give you bonuses but give unhappiness for
Now, granted, a lot of the stuff I mention is essentially more of a different game. I don't want to be like cities: skylines and have to manually plan which districts are connected by my city's metro lines, but it would be nice if there was a little bit more that builders can do in the modern era. Heck, you can even make the game scale even more exponential than it is now - the modern era should be exponentially longer than it is now, so maybe it should be the case that a modern university should give as much science as 20 ancient universities. But might be a neat mechanic where essentially everything changes when you get to the industrial era - suddenly your old commercial hub doesn't cut it anymore, and you either need to upgrade it to a modern one, or leave it around as a tourist attraction and build a new modern commercial hub somewhere else instead.