I would suggest trying the "Legendary Material" Variant that I created for my tables. It's simple, but need some criativity from part of the master and the players.
It is a 3-step process, and it goes like this:
Step 1: Research
The players research a library, buy a scroll from a wanderer, found the schematichs in a stash. Somehow, they are handled a hint on how to give a property to an item.
Extremely grateful for being saved from the giant ants, the Old Sage gave you guys a
scroll containing an ancient ritual to imbue the Power of Ice on the blade of a sword.
The king gives you access to the journal of his father, so you can investigate the origins > of the evil that lurk the land. While you were reading the journal, you learn that his
father created his Holy Sword by taking his blade to an Angel that lives at the top of the
Mountain of The Fallen.
Put that "recipe" in a real, paper notebook, and hand it to the party, detailing how they put those powers in their weapons. You can use things like "A branch from the holy tree of the country XYZ", a "drop of blood given of free will from a Iffrit", or even no materials at all, but a place and a time - "Present your blade to the gods on the full moon of the fourth month of a even year".
That way, you can control exactly what powers they will have, insert tons of fluff in your campaing and break totally that ideia that "money = power" that D&D tends to give.
Step 2: The Quest for the Item Property
Let the characters embark on a subquest for they holy blades or their flamming spears. Let them hunt the Golden-Horned Minotaur for it's unique horns, let them kill the Queen Wasp for her miraculous honey, let them defeat the Monster Garden Gnome of Doom for... hm... his ceramic hat. Drive them into a quest and make it HARD. Make them feel connected to getting that item enchanted. Make the item feel Special.
Step 3: The Discovery of New Powers
And... then, do something really special for them. When they finish the subquest, make them emerge with not only a holy blade/club/belt/spear/underwear, but whatever they may get during the way and a whole new set of unexpected powers to the item they went to imbue.
Make creating an item something hard, an adventure on itself, and your players will get really happy when they finally put all the pieces together. Then let them use they new powerfull item, and let them have fun!
You don´t need to get stuck with the Magic Item properties. Create yourself new, interesting things. Create powerfull itens with strange drawbacks, or itens that happen to change powers depending on the situation.
Even better, let the players try things. Let them loose to try things by trial and error, and if you think that some mambo-jambo they tried seens worth of a magical property, give it to them. You don´t need to "rulify" it too much. The more you incentive the players to do things by thenselves, more interesting the game tends to become.
Also, I wouldn´t recommend tying skills in that way. Skill points are a scarce source, so unless you pretend to give players more skill points per level, there´s a good chance that craft skills will be ignored. A good way for that to work however is granting everybody a few "Special Skill Points" every level, up and above the normal skill points, that could be used only on Craft, Knowledge or Profession. That way players will spend points on those things, and you don´t incurr the risk of getting into a Skill-Based Dead-end.