The theory is that Mewtwo will spawn or will be obtainable via new structures-haunted mansions.
I refer you to the last post of this page: viewtopic.php?f=12&t=1396
I refer you to the 4th post of this page: viewtopic.php?f=12&t=9 (note that it says "according to". This would imply SPG didn't know, and then you consider that the other post was made after this one.~after he found out the plans for it)
I refer you to the Cinnabar island mansion and subsequently the journal of Mr. Fuji in the basement-the one that describes the creation of Mewtwo and its subsequent rebellion~
http://bulbapedia.bulbagarden.net/wiki/ ... n_journals