Im all for Riot releasing recolored palate swaps for champions, Frosted Ezreal is his best skin, Mercenary Kat is second best to Kitty Cat Kat.
The problem with your idea would be the lack of splash art to go with the color. Also since you'd want every champ, every skin to have access to color modding, riot would have to make a program or color editing tool for each champion and for each skin. Seems a grand undertaking for small gain.
What Riot should do is get the base model of a champion, mix and match colors that look unrealistic but awesome for certain champs, pay an artist so make a badass splash and done-deal. Such as! Brands flames are neon green, id pay mad money for that (but not Brand as an ugly ass zombie >.>)