The
CE People Modified Addon does a similar thing. Nice that you thought about the colour blind variant as well, I actually completely missed that till now.
Some suggestions if you want to do more complex recolours:
1. You can rework some sections of the sprite selectively to achieve more distinct looks. Colour select tool (in Gimp, exists in Photoshop as well for sure) is very helpful for this. You can edit the blades of the mantis or the uniforms of humans separately for example.
2. The crew combat projectile in the lower right corner can also be changed freely. You can modify its shape, add glow and stuff... A lot can be done with that, the vanilla projectiles are some of the least detailed assets in entire FTL.
3. Adding glow is another thing that can make the skins more distinct. Makes sense specially for Zoltans or the light sheets of the battle drones. In Gimp you can use filter/drop shadow with x=0/y=0 to produce nice even glows around things.
4. You can change certain frames separately to create interesting effects. My first try on that was a skin that makes the Slug cloak as long as it walks or fights... Much more could be done with this I guess. Crew could activate personal shields in fights, Zoltans could glow more during certain activities. This would be purely visual effects of course, could not have any influence on actual gameplay.
