>>14248700It's confirmed Mewtwo was made in the Cinnabar Lab. The books, the statues of Mewtwo, Ditto being failed clones of Mew (Same colors, even shiny colors, weight, transform, and of course them being failed DNA blobs). Blaine is the only remotely important character on the island and is a scientist, Team Rocket has scientists and is the only one with the ambition to produce Mewtwo. Giovanni has little other reason to want to bother with getting the Master Ball from the president, either, he's going to go reclaim his presumably rebellious Mewtwo. The Cinnabar Lab is abandoned because Mewtwo wrecked it and left, no reason to just not use a perfectly good lab.
Then you realize the other media has Team Rocket/Blaine produce it in the lab via anime/manga and it's just painful to not assume he did it.