I guess it's just to keep Cubone's face a mystery. It would be nice in future games though, if the developers coded it different, so that Day Care Cubones didn't have skulls on when they hatched :)
Yeah, that would be cool.
It would also make more sense, really. Isn't it that Cubone wear the skull of their dead mother? (Of course, if the WMG that the players make up the Pokedex entry is true, then case solved. But otherwise...)
As for what I think the most mysterious Pokemon is...Unown. They're just weird.
And should be involved in more event things.