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I don't dispute that Arceus created the world. Well, I would dispute the claim that nothing existed before Arceus (I believe that at least the Unown predate it), but that's beside the point. And yet the question remains: Should Arceus be brought up in the context of Mew's origin? If it wasn't directly involved with its birth, then the answer is no.
Cynthia did briefly mention that her reason for visiting Undella Town was the underwater ruins, but she didn't seem to make any effort to actually explore the ruins (she always seemed to prefer to battle the player or talk about unrelated things). Personally, I would much rather see the Abyssal Ruins mystery be solved by other characters, especially as I believe it is directly relevant to the main story.
Arceus is believed to be the origin of the universe, which is not the same thing as being the common ancestor of all or even most Pokémon. As far as we know, Arceus only created the Creation and Lake trios. Did it directly create Mew? I would think not. Arceus was said to have gone into an unyielding sleep after the world was created, and it seems most probable that Mew was only created later. The original dragon was born in the Dragonspiral Tower around 3,000 years ago, so it is fair to say that Arceus had nothing to do with it. Mew almost certainly dates a lot further back (we know that Genesect and the fossils do), but we can infer that Arceus wasn't actively involved by then.
And do you think the themes surrounding Mewtwo & it's creation would conflict/line up w/ Genesect & it's possible release, in it's current form & the form it was before being modified?
It would line up with it. I think most fans are bothered by Genesect retreading the anime Mewtwo story, so Game Freak should prove that Mewtwo wasn't created for Team Rocket in the games. Not only that, but it would be interesting to explore how different Mr. Fuji is from the scientist who resurrected Genesect, who confesses in Black and White to being solely interested in Genesect's power. Mr. Fuji is obviously a much more layered character, so even though it might make Scientist Dudley look bad in comparison, the differences should be noted. Finally, Mew is very different from Genesect, since the latter was a hunter even 300 million years ago; the resurrection only made it stronger (or so Dudley thinks).
But I remember hearing on some podcast (not sure if it was Bulbacast or not) that maybe having Mewtwo be part of a storyline again would be a bit old or something along those lines.
I'm guessing it was in reference to the anime, but it doesn't really matter what they said unless they provided convincing reasoning. Mewtwo's story in the anime was indeed wrapped up in Mewtwo Returns, but the in-game Mewtwo's story was barely touched upon. What I hope to see in B2W2 is a Wi-Fi event on Faraway Island, where Mew will be catchable and Mr. Fuji will tell us his story.
I'd like for there to be an answer, and Mewtwo's existence/emphasis would be a good nod to the whole "bringing old Pokemon to Unova", but has there been something in any of the games that indicate whether Mr./Dr. Fuji has been up to something since the events in Lavender Town?
He wasn't referenced in Black and White, and he was still living a quaint life in HGSS. I don't think he is up to anything; he is a kind man with a sordid past, and I believe that he has been trying to redeem himself after what he did to Mewtwo. Since he was already old in the first two generations, I can only hope he isn't dead now. Of course, if Game Freak want to solve the mystery, then he'll show up regardless of his age.
I have a theory that Cedric Juniper may have worked with Dr. Fuji when they were younger. I have no evidence for this, but it would a neat revelation as Cedric's daughter, Aurora, is interested in the origin of Pokémon; Cedric also tried to get Skyla to take him to another region (Skyla turned him down and she mentioned that places like Kanto and Sinnoh were too far away). Aurora would definitely be interested in Mew, and it is her father who pushed her in that direction.
yeah though to me Max is a drawf Nine year old dispist people saying he seven, honestly why wousl a mother allow her son to travel with hsi sister and friends if he seven, that just wrong and at first I hated Max but saw Mira episode in Japaness and though, "she a female Max but taller. I like that." and jsut ship them together, and yes I calling Mira and Max the same age as one Mira stated she was in school/trainer school and she and her friends want to be trainers so how can you be a trainer when you are a trainer? so she can't be ten years old.