Update March 30, 2018:
In reviewing these old questions I realize that this request has been fufilled for quite some time. The macOS version of LuckGrib saw the addition of some routing features in version 1.2, and you can create waypoints in several ways.
Since adding that work, I was asked frequently if I would support being able to name the points, or change their colors. These abilities are now available in the new iOS version of LuckGrib. Look for the this additional capability to appear in the Mac version of LuckGrib later this year.
As a sailor, I see the value in being able to create a number of waypoints to mark interesting locations (destinations, turn points, your boats current location, and so on.)
There are going to be new versions of LuckGrib, and at some point in the evolution of this application this point is going to be addressed. I can not make promises on dates on when this will be available, but as the author finds the lack of ability to create waypoints frustrating, and the author is actively using this application as he cruises, this is going to be solved.
Please be patient, new features will be appearing in the future.