I wouldn't say that Mr. Fuji had a "temporary" interaction with
Mew; Fuji's diary states that he discovered
Mew in Guyana (most likely Faraway Island) in July, and it was only in February that Mew gave birth. Who knows what transpired between those events? For all we know, Mew could have been taken to Cinnabar, only to be brought back to its home when Fuji gained his senses.
What I had in mind was something akin to
Celebi and
Ho-Oh's appearance in Colosseum. They had a connection to Orre, but they didn't live there, nor were they canonically caught by Wes. Colosseum and XD are the only spin-off games that don't make it hard to believe that they could, in fact, belong to the same continuity as the main series. The only way the new game could ruin that is by making a ridiculous amount of legendary Pokémon conveniently available (like some other game series I won't mention), or by failing to acknowledge
Mewtwo's origins (should it be brought up at all).
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