A big part of making feasible games (ones you intend to finish) is cutting features to limit the scope of your game. During Unicorn Quest's development a lot of things hit the cutting room floor. One of my first ideas to go was the customizable hero. I tried thinking of ways to make it work but in the end it just required too much work and too much game memory.
Players were going to be able to dye Clover's hair, coat, and cloak with magic dyes you could buy from shops. This came from me wanting a way to allow players to make the protagonist they want to see. Mainly because I wanted there to be some discrete way to make Clover purple for those who wanted her to resemble the character she's based on.
As far as execution it would just be a matter of recoloring sprites in Gimp. The problem comes from memory. There can't be hundreds of sprites in the game's data for just one character. Android apps should be kept as small as possible.
I was going to layer the sprites so that Clover, her hair, and her cloak were three separate sprites that moved in sync. That way, I wouldn't have to make spritesheets for every possible color combination. I tried to make the idea work by making her cloak cover her mane and tail, but the design was ugly and I began to love the Faust style default color pattern.
In the end I'm glad I did it. The game will be much smaller now which means I'm more likely to finish it in decent time. Deciding on Clover's permanent colors is also good for the game because it separates itself from the source material. Clover feels more like her own character and not just a clone of somepony else. I think this will make her more memorable in the end and that's what I want.
I often hear that characters should be designed with silhouette recognition in mind. Interesting shapes and color combinations that contrast nicely with the environment makes characters like Mario and Link so memorable. That's why clover is highly saturated, bouncy, and wears a hooded cloak. It makes her stand out, makes her easy to spot, and makes her easy to draw.
I want Clover to be my first mascot. A character players can fall in love with and want to see more of. My mission is complete the second I see fan art.