Here's some of my ideas when I was playing AOK, but they were overealistic, and since I got AOM I've realized that such things seriously makes games less fun.
1. Mining is possible by any vill on any square of land: but those doing it on 'mineral sources' will get, say, a 10x gathering rate? Mineral sources are exhaustible, but they can last quite a long time before running out.
2. You can build bridges, make roads and open canals
3. Most land units can walk in shallow waters, as well as light vessels, but heavy ships cannot
4. All warships can be garrisoned, and gives the same bonus as they gave to buildings in AOM and AOK. Also, troops can be used to board enemy vessels
5. Capturing of enemy buildings: each building has a certain defense point. You can set multiple troops to try and attack and capture a building using a certain button. The building's HP will decrease at a much slower rate, but its defense point will fall. When it reaches zero, the building is captured soon, depending on the number of troops attacking and the number of units garrisoned in the buildings. Garrisoning makes it more difficult to reduce a building's defense, and makes it take longer to capture even after defense reaches zero. Defense point slowly regenerates, more garrison means faster regeneration
6. 'Salt water' and 'fresh water'. Seas and oceans are salt, rivers, lakes and canals are fresh. Farms near fresh water sources are harvested quicker, as are farms near forests. However, forests give a mining penalty.
7. Roads can be built, which increases movement speed.
8. Different units have different speeds on different terrains. Roads eliminate terrains.
9. Gatherer and builders are different units.