It's a dilemma. ZOS doesn't want us to only use transmutation to get the right gear but instead it is supposed to help make the grind more bearable. They don't want us to be able to "have them all" but also don't want to clog up our inventories.

As a tip for you, if you find yourself drowning in gems, transmute weapons to nirnhoned and deconstruct for a chance of getting nirncrux. That way you can at least make a profit.