You need to come up with a base design first, or several to cater to a specific function each, and not allow variance from there. Then you can customize portions like rubber, lined or unlined, Velcro or laces, and colors.
The more you allow the design to change the more expensive and lengthy the build per shoe will be.
Heck, you will probably satisfy the masses if you allow custom color selection only.
Look at what Wild Things does with their custom garments. Pretty cool stuff, I built my own wind pro hoody in the exact colors I wanted on a kick ass base design.