**NOTE** - I have posted this about five times in the thread and still no one seems to get it. I DO NOT THINK THIS THEORY IS TRUE. It ca't be true, otherwise the people at Pokemon would have said something about it. Its just a neat theory to ponder.
So I was looking up some info. on Cubones for a story I'm writing and I came across this video on youtube. I know this is probably exploring Pokemon deeper than need be, but the video actually makes some sense.
Basically the idea is that a mother Kangaskhan dies, leaving its Kangaskhan cub on its own. The Kangaskhan cub uses the skull and a bone from its mother to use as protection and becomes a Cubone. Then through malnutrition or adapting to a different lifestyle, the Cubone evolves into a Marowak.
This could explain why Kangaskhans are endangered, because some of their cubs are being turned into Cubones. I don't believe it says anywhere that the mothers of Cubones are Marowaks, except for in Red/Blue/Yellow when you have to calm the mother Marowak spirit. But, there could also be Cubones that come from Marowaks and Kangaskhans, which could explain why they are so common.
This is just my input, but Marowaks seem like they are more 'hardened spirits' and don't really seem like they are the parent type.
My 2 cents.