Detective Barricade:
It's still a bit of an odd the way they worded it. Also note Mewtwo's Pokedex entries in the original Gen I games:
Mewtwo Gen I Dex Descriptions said:
It was created by a scientist after years of horrific gene splicing and DNA engineering experiments.
To me that sounds like the took Mew's newborn and experimented on it. Gen II makes no mention of Mewtwo's creation (besides Crystal saying it was "created solely for battling"). However Gen III had some oddities with its Mewtwo dex descriptions. RSE and LeafGreen stuck with the gene splicing and DNA manipulation story, but FireRed had a new dex description:
Mewtwo Gen III Dex Descriptions said:
Ruby & Sapphire: Mewtwo is a Pokemon that was created by genetic manipulation. However, even though the scientific power of humans created this Pokemon's body, they failed to endow Mewtwo with a compassionate heart.
Emerald: A Pokemon that was created by genetic manipulation. However, even though the scientific power of humans made its body, they failed to give it a warm heart.
LeafGreen: It was created by a scientist after years of horrific gene-splicing and DNA-engineering experiments.
FireRed: A Pokemon whose genetic code was repeatedly recombined for research. It turned vicious as a result.
FireRed is the first to pretty much say Mewtwo was made from Mew's genes. Not admittedly the other dex entries are ambiguous about exactly what kind if gene slicing and DNA experiments went on. They could have experimented on a newborn Mew/Mew Egg or they could be messing around Mew's genes. However a thing to note about FireRed's dex entry specifically mentioning the recombining is that most of Mewtwo's future dex entries talking about its creation mention it was made from recombining Mew's genes and nothing on the gene splicing and DNA manipulation (except for those entries which were copy & pasted from old dex entries like X's and ORAS).
Also, the dub of Origins changed the wording of the Pokemon Mansion journal entries (the Japanese kept them the same):
Pokemon Mansion Entries said:
Original: A new Pokemon was discovered deep in the jungle.
We christened the newly discovered Pokemon, Mew.
Mew gave birth. We named the newborn Mewtwo.
Mewtwo is far too powerful. We have failed to curb its vicious tendencies...
Origins: Today, while on our journey through the densest part of the jungle, we were surprised to discover a new Pokemon.
We decided to name the recently discovered Pokemon Mew.
From the potential within Mew, we have managed to create an entirely new Pokemon: Mewtwo.
It has become far too strong. It is beyond even us now.
The dub made it more clear Mewtwo was created and not born from Mew. Actually, rereading it makes it sound like the scientists impregnated Mew, ew.
Mewtwo being a clone is the current canon, I don't think anyone is denying that. All I'm saying ORIGINALLY it sounded like maybe they had another idea for Mewtwo's creation, maybe even going along the lines of how actual cloning is done (FUN FACT: Originally there was going to be a Pokemon based on Dolly the clone sheep, however they felt that would be too controversial. Dolly was created by taking an egg from one sheep, a mammary gland cell from a second sheep, and carried to term by a third sheep. So while they scrapped the Dolly Pokemon, they could have possibly kept the real cloning process and quietly recycled it as Mewtwo's original origin).
Anyway, as for Cubone, maybe there could be a bit of truth to its Dex description. Maybe while not directly its mother's skull and femur, a newborn Cubone skull and bone club maybe are external skeleton which shape matches that of its mother's skull and femur. As for Cubone's mother dying, maybe
WaffleTitan has an idea that for some Pokemon they can give live birth. Pokemon Eggs always seemed a bit... artificial, at least the Eggs that we know. Maybe people found a way to artificially stimulate a Pokemon to reproduce that is not the natural way they reproduce. Pokemon in the wild would still mostly need to rely on their natural reproduction methods and maybe its those Marowak who die upon giving live birth and Cubone mourning their deaths.
Perhaps that is what most legendaries do: give live birth. That requires a lengthy gestation period, which is just one more reason why legendaries won't breed in captivity.
Possibly, also it could be the way Legendaries breed can't be done artificially or they just outright refuse to breed in captivity. Many Legendaries are also long living, they don't really need to breed that often, maybe once every century just to have a backup just in case something happens to them and they need to be replaced.
There is only the question of Manaphy since we know they come in eggs. Also, why do Manaphy in captivity produce Phione?
Hmm, are we sure the "Manaphy Egg" us an Egg? It doesn't look like a normal Egg, and when bred in captivity they produce normal Eggs that create Phione.