The Rome at War mod makes naval combat interesting not by buffing the units, but by giving us more reasons to fight on water.
1.
Being able to build walls and sea towers actually lets you control and take territory without physically occupying it with your navy.
2.
The more diverse economy (i.e.
not all ships cost only wood and gold) makes it easier to incorporate water battle into land battle.
You can see this in effect on land with “one unit civs”, usually archer civs, who are boring to play because they can only do one thing well.
Britons and Mayans comes to mind, Burmese/Bulgarians/Spanish.
3.
The mod team said they’re planning on making more ocean resources, such as deposits of gold and stone, which gives further incentive to actually fight on the water.