A bone to pick with cubone...(pun intended)
So, yes. My interpretation. Cubone, the lonely pokemon. The mother dies after birth, and although Red, Yellow, Blue implied poaching, I think it is safe to say that at this stage it isn't even a remotely realistic theory. Complications during labour is a decent theory in my opinion so I accept it.
Seeing as I am a romantic, I tend to want the lonely essense of cubone not to be lost when transfered to a more realistic version of the pokemon world. The pokemon still pines for its mother even though it happens after every single birth. It probably sees no flaw in carrying its mother's bones, its mother carries her mother's bones and so fourth, so it think it is safe to assume it thinks it is a way to be closer to his mother.
And then, once it accepts its mother's death fully, it trains, to protect others, through art it looks like the skull basically fused to its head. I am fine with the whole fusing skull thing, never been that strong of a realist anyway.
Then after finding a mate, a hard thing to do, another cubone is born. What happens to the father? Especially if it is a marowak, as a marowak is a guardian pokemon, and a guardian wouldn't just mate and run away from the baby, I would assume. Well, we could remove the mother bit and say that parents give birth to two and both parents die, but then cubone isn't as lonely seeing as it is with a sibling. This solves the whole, the female sex disappearing thing. But it also ruins the typical cheesy story that is every life of a cubone which I love very much so. So, I assume that the father has it a bit off on the instinct side of things and doesn't stay to witness the birth of the child.
Now, about the whole skull not looking like marowak's head. I call that design flaw. In Red and Blue, sprites were rather vague and open to interpretation so as it was around that time that the cubone line was created, perhaps the designer's did intend marowak to look like that of a skull of cubone. But I doubt that seeing as the anime didn't just make their own interpretations based on sprites, they most likely worked off art given to them specially. So, why does marowak's head look nothing like cubone's skull? Well, I wouldn't go as far as saying that it looks nothing like it, but yes, they do look rather dissimiliar. Still, however, I say it is just a simple and rather quirky desistion by the designer. Why? Well, I don't know. But I can safely say that my interpretation is that the skulls are in fact the same. My interpretation may not be perfectly in canon, but it suits my needs.