Bigger maps!! Maybe 20000-40000 squares!
and more tech, more wonders (but not too powerful wonders, like CIV:CTP, it should be live civ 2 wonders).
It is quite natural for ships to sail on both rivers and the sea. But it is only some ships, which both sail on the ocean and rivers or just rivers or just the ocean.
Most oceanic ships cannot sail in shallow waters and very small ships cannot sail the ocean very well.
The engineers should be able to modify existing rivers too, that should be less expensive in resources than building a brand new canal. This could be very useful, and it should be a very expensive option. Maybe a new Wonder would be good to introduce here.
Minefields at land and in water. The watermines could start to float! Nobody knows where the mines is, they are not visualised on the map. Workers in cities might get killed.
And a people counter that can count to more than 320 million people!