Obviously this is a very low priority at this moment, but Foobar's second image in his last post summed it up nicely. Look at the two different ship sizes in that photo. The larger ship v.s. the waves looks just about perfect.
I'm not a programmer, but wouldn't it be pretty simple to just set the waves textures to 1/2 scale and the same with whatever programming generates the waves?
waves.ini
waves enabled = 1 (value)
wave scale = 50 (percent)
wave speed = 75 (percent)
waves detail level = 5 (value)
wave nitpicking = 1 (value)