Most head units are way more suseptable to skipping unless you its an MP3 unit. If you stay with just a head unit without a CD changer, you might consider an MP3 unit.
If you plan on a changer, I would recommend swapping your Alpine for a Sony head unit and purchasing a 10 disc Sony MP3/CD changer model number 757MX. It has 12 second antiskip memory. I have never got mine to skip no matter how rough the water is.
Another side benefit to the Sony is a wired marine remote is available for most head units. Adding a few of those would allow you to control the stereo for virtually any location in the boat