There is a discussion going on about wave height in this thread
http://www.subsim.com/phpBB/viewtopic.php?t=46709, and one option in the new SH 3 Commander could be to have waveheight changed due to season, lets say 1.0 in jun-jul, 1.25 in aug-sept, 1,5 in oct-nov, 2.0 in dec-jan (winterstorms), 1,5 in feb-mar, 1,25 in apr-may etc.
This could simulate weater-conditions during a full year and be an option you could choose.
What do you think?