No it isn't. You're just overscrutinizing it under strict real world logic. Next youll tell me seaking Is a moronic design because fish can't be on land or conjure up impossible amounts of water for its moves.
Its a schizo tangent. The "cubone storyline" being praised as an example of gen 1 having a more interesting story was not about the generalized Cubone species and its relation to their moms bones(though it reinforces the theme), it was about that specific plot since it deals with Pokémon murder in the context of Pokémon exploitation by Team Rocket and showing Fujis redemption raising a mistreated Pokémon in contrast to how he "raised" Mewtwo.
A species known for using its dead parents bones doesn't make Cubone feel like a character. A Cubone having it's mom murdered that turns into a vengeful ghost that needs calming and being raised by a repenting man does make it feel like a character, and it should, because that specific cubone IS a character.