The size and depth of the waves are controlled by the SeaWater.fx file in your shaders30 folder.
It can be opened with any text editor, and you will find the BaseOpacity, WaveBump and WaveScale parameters at the top.
Lower numbers make the water more transparent, the water rougher, and the waves closer together.
The overall look is strongly influenced by the WaterDetailTextureSize setting in ConfigOverrides.xml created by running cfs3config.exe and going into the custom settings texture info section.
In 2014 I had my settings at 0.95, 0.8 and 1 with Texture Size 5
In 2015 I changed the values to 0.95, 5.0, and 5.0 with Texture Size 5
In the 2016 Beta I'm using 0.95, 5.0 and 2.5 with Texture Size 4
It's really all about trying different combinations until you get it to look the way you want.
I seem to recall that there were also some changes relating to how the sky reflects off the surface, and the sea foam rendering that happened between 2014 and 2015. Gecko was recently looking at the wave textures themselves to enhance the sea foam functionality (any areas in alpha layer >140) for use with the 2016 Beta.