Layonara does not use the craft skills, craft trap, craft armor, craft weapon.... etc.. at least not to actually craft such things.
Craft Weapon and Craft Armor have a use they help you to succeed in changing the appearance of your armor and weapons.
Crafting is Stat based. Example your level as a crafter, your Dexterity, and your Strength determine your % to make things in Woodworking, and most of the metal crafts.
Dexterity and Charisma - Gem crafting...
and so on.
This topic has been answered a few times before. If you feel your points are wasted I'd say post in the greivance section... worst case they say no and your where you are now.
G-452