I was having the same problem for a while too. I use my Macbook as a tv when I go to sleep. I just throw a bunch of videos on my playlist and go to bed. I was sick of constantly pressing "C" to change the crop. I don't know if this way works for everyone, but this is how I got mine to default it's crop to 16:10.
Make sure your VLC player is up to day. Then simply go to: VLC player preferences > video > Then enter in "16:10" (or whatever crop you want) and then click save.
Good Luck