I have a sort of head spinning theory, first I refer you to Mew, and its uncanny similarities with Ditto, Same color sprite, both smile in their sprite, same weight, both have same color shiny sprite, and Ditto are located where Mewtwo was created, and where testing to clone Mew took place, Cinnabar Mansion, also, Dittos are located in the cave in which Mewtwo is located in Red and Blue. Now I draw your attention to the pokedex and its numbering process, which should be ordered in chronological order, the order in which the pokemon themselves were discovered, Mewtwo's number is 150, whilst Mew's number is 151, even though if Mew was not yet discovered, how could a clone have been created? I thank you for keeping with me, you only need to for a while longer. Mewtwo's tail has the exact same color as Ditto does on its own, and the rest of its body is a very plain color. I believe that Mewtwo was the original Mew, but the creators wanted something simpler as the mysterious pokemon, hence Mew was created. Also, Mewtwo seemed menacing, so if Mewtwo was a clone, the creators could give Mewtwo a backstory to give it a reason to look menacing. The change happened at the last second, so the Pokemon creators just put Mew as number 151 and left it at that, and later on, made the possiblity to find Mew not possible until an event was made, in which the event stabilized Mew, and made it possible to be caught without wrecking the game.
Any ideas on how to improve? This was off the top of my head, so I'm sorry for any inconsistencies.