It depends on how you want the Skills to work and how you want the players to purchase them.
If Custom Skill gives you what you need for the Skills you have in mind, then a prefab is likely the best/easiest way to go. Similarly, if existing Skills are close and can just be renamed, you can use a prefab for this as well (though the players may get some odd repeat purchase warnings for some).
If you're after more robust rules logic for your Skills or want to create a more elegant/seamless renaming of existing Skills, then a custom template is going to be the best option.
In terms of purchasing, if you're after a package deal like structure (e.g. "all navigators will have the following Characteristics and Skills"), then you'll want to look at creating templates for each of them (defining the starting character traits for each one). If you're after more of a "choose 3 of the following Skills" type of purchase, then appropriately named lists within a prefab is your best option.
