See, I still do regular art! I'm actually really happy how this guy turned out! Except for the leaf, though... >.>
Anyway, my theory is that rock pikmin are like turtles/hermit crabs. The seed, when planted, sends out a signal that causes minerals to form around the pikmin. After they are plucked, they use mud like mud daubers to repair any holes or cracks in their shell. If they outgrow their shell, then they just make a new one using any nearby minerals (like the rocks the skutterchuck throw).
Took about 30 minutes, and it's on bristol board using a sharpie.