Quoted By:
itt people unable to comprehend the plot of a game geared to six year olds
Nothing says that legendaries are unable to breed period, just that they can't breed with the mons that we know of. Their egg group is called "Undiscovered", not "Unbreedable."
Mew is said to have given birth. Mewtwo is said to have been genetically engineered from Mew. Taken together, it means that Mew was artificially inseminated and gave birth to Mewtwo. That's how you would genetically engineer a creature in the real world; through artificial birth.
Whether or not the scientist was speaking in metaphor can't really proven or disproven, but I don't see a reason why to assume he was. A couple of Pokedex entries state that scientists believe Mew to be the ancestor of all Pokemon. So scientists do think Mew can give birth, and there's nothing saying that legendaries can't give birth period, so there's no reason to think the scientists were speaking in metaphor.
Mewtwo is most likely a clone. Genetically engineered from Mew, said to share almost the same amount of DNA as Mew, and is even named "MewTWO."