I like what you've tried to do with color crystals, but I have an idea that might make the system a bit more flexible. I personally like the traditional lightsaber colors - red, blue, and green. I don't have a problem with other colors being in the game, but I prefer to use those colors on my toons. That said, right now, I can't if I want the best stats.
So here is what I propose - Let us unlock colors much like we unlock titles. Once we've unlocked a color, we can apply that color to an existing crystal. The crystal itself would host the stats. Let us permanently unlock the colors so we could do it as many times as we wanted.
With this system, guys like me who want to use the "basic" colors could do so without facing a state loss. I think you could also incorporate legacy into this, ie if you get to legacy level 50, you unlock hot pink or some other crazy color.
Thoughts?