Another awesome custom has popped up, this time with Photo Finish.
This right here is how you recolor a pony! Lets do it Hasbro! I'll even advertise them here for you.
If you are interested in making your own, the Twilight Sparkle toy in the5 pack is probably what you want to mold it from. Photo finish is actually a recolor of Twilight in the show too, so it works out nicely!