My skill with rigging is somewhere between novice and intermediate; I can say from personal experience that rigging a character is a tedious task, but it's definitely worth the effort in the end. Since these are for 3D prints, I can understand why a basic rig at most would be used. It sounds like you made a type of proxy mesh base for the pony's body, and recycled parts for other similar models. Smart move! Why remodel from scratch when you can save time, money, and effort by recycling what you've already done?
When you're more comfortable with character rigging, I bet you could make a fully rigged and weighted pony body for each type; filly, colt, mare, and stallion versions of earth, unicorn, pegasus, and alicorn (royal & young) ponies. Then, for coloring it's just a simple exchange of shaders.
Easy-peasy puddin' in the freezy.