I felt like posting a few weird Pokémon theories. So shut up and listen.
You killed Blue's Raticate (RBY). You monster. Ratatta, and later Raticate, is a primary 'mon on Blue's team right up until you flatten him on the S.S. Anne. The next time you meet him, he's in Lavender Tower. And he doesn't have much reason to be in Lavender Tower - given its full of unidentifiable ghosts that can't be battled. But he doesn't have his Raticate any more. And never will have for the remainder of the game.
Ditto is a horrible scientific mistake (RBY). One of the sub-plots to RBY is the scientific efforts - and continual failures - to successfully clone a Mew. Whilst success is ultimately achieved - with Mewtwo - you have to wonder what happened to all the failed attempts. Enter Ditto. It's regularly found in Cinnibar Mansion (the place where clones were attempted). It shares the same colouration and weight as Mew, and future generations would also match it with the same shiny colouration too.
It is often described as having highly unstable DNA that can transform into other Pokémon - but some Pokédex specifically state that if it tries to transform itself into something by relying on its memory, this POKéMON manages to get details wrong. The Cinnabar scientists never discovered a real Mew, and so the cloning attempts continually go wrong. Mew and Ditto are also the only Pokémon to learn Transform. Ditto are the failed attempts to clone Mew, broken Eldritch Abominations discarded by scientists, to live a tragic, identity-less life.
And to get their funk on with almost every Pokémon in existence.
Cubone > Marowak > Kangaskhan - These two families have always been a bit of an oddity. Cubone claims to wear the skull of its deceased Marowak mother; but anyone who's bred a Marowak will know that it doesn't die. Nor, mercifully, are players ever treated to a scene of Cubone tearing out its mother's skeleton. Marowak also wears a skull, the origins of which are never explained. There's one simple (and much more likely) theory that what is actually meant by "Cubone wears its mother's skull" is "Cubone wears the skull helmet that its mother once wore" - ie, the skull belonging to the mother, not the one that's actually part of the mother. But I prefer the other, slightly darker theory.
As for Kangaskhan, it has that little baby in its pouch. Even if you hatch a Kangaskhan from an egg, it comes already with baby in tow. Which is... weird. It hasn't passed people by that Kangaskhan's baby bears more than a passing resemblance to Cubone sans skull. And Kangaskhan could certainly fit in Cubone's evolution tree without looking particularly out of place.
So the theory goes that Cubone were originally orphaned Kangaskhan babies, and the skull belongs to Kangaskhan. Morowak would represent the orphan as a teenager (and not Cubone's mother), before finally evolving into Kangaskhan when becoming a mother. Appearance-wise, there's the old media stereotype of the active, rebellious young woman (Marowak) having turned into the uh... rather large, extremely protective, frumpy woman upon having children.
. They just (kind of) got the appearance right. 
(Unless we see an RS remake which would still hardly make up for being on long-outdated hardware in my opinion- as much as I love Hoenn...)
