2. Mew and the mysterious message in Pokemon Emerald
In Pokemon Emerald, players could obtain an Old Sea Map via an event and it would allow access to a place called Faraway Island. On this island was a wild Mew. Now, before the player enters the forest area where Mew is found, there's a sign that reads...
"The writing is fading as if it was written a long time ago... ...ber, 6th day. If any human...sets foot here...again...et it be a kindhearted pers......ith that hope, I depar...".
In the Japanese version of the game, this message is mysteriously signed 'ji' and the first half of the name is missing. The only character in the Pokemon universe that really fits the signature is our Kanto friend Mr. Fuji, who was known to be involved in Mewtwo's creation.
With this in mind, it appears Faraway Island holds the Mew that was used to create Mewtwo (as mentioned in Cinnabar Islands diary entries) and was brought to a remote Island out of harm's way. Granted this is a bit of an assumption, but it's very intriguing nonetheless.