In a properly built game, not at all.
You just have to build the game for the customization process.
I haven't seen too many games use this, but those that do tend to use it well. Rune Factory 3 is probably my favorite. Crafting gear in that game rocks. The further you get, the more the game expects you to have custom gear. But there is no "right way" to customize it. I've seen people go to town with a single hammer that paralyzed enemies to allow the player to get around the slow speed and dish out massive damage. I've seen people use a spear with knockback to keep everything on its butt from yards away. I've seen people use staves imbued with ridiculously awesome attacks gained from bosses. I myself have used several different effective customizations to my Double Blades, no one of which is really any more powerful than the others. It's just a question of how you customize it, and what play style you use with it.