Are the colors really going to be red, yellow, green, and purple? Purple looks very ugly and out of place if you're only going to have 4 colors. Blue would be the right color, making it red, yellow, green, and blue. I also wouldn't mind seeing more colors because 4 feels very limited.
I prefer the WoW gem system over this current one. Red boosts the 3 primary attributes (Strength, Dexterity, or Intelligence), yellow boosts your attack rate, crit chance, or dodge chance, and blue boosts your Vitality. Orange, green, and purple are mixed colors and give stats from what they're mixed with. This gives you the entire rainbow spectrum (red, orange, yellow, green, blue, purple).
The helm bonus for Amethyst also needs to be changed, because all of the gems except Amethysts do something different on helms over other gear slots. Since the Mystic is removed, this is also an opportunity to have more interesting helm bonuses like the WoW meta gems.