Clear crystals give you the power to do spells, whereas the colored ones give you at-will abilities of that type. The clear ones are weaker and lose their power over time. Therefore you need special materials (think eye of newt) and the complex geometrical patterns drawn on the ground and all that time and prep and precision. This ensure's it's done right the first time, focuses the magic it perfectly, and prevents you from wasting any power. Only the most brilliant, studied, and well-funded scholars can actually invent new spells due to the scarcity of the crystals.
