There is the theory that Ditto were created in experiments in the Pokemon mansion, when they were trying to create a superior Mew.
Some of the most prominent locations it appears in include the Mansion basement and the Cerulean cave, where Mewtwo hid.
Eh...I'm not sure. I think that's just a coincidence. The original story of Mewtwo in RBY was that the scientists captured a Mew and impregnated it with Mewtwo, to which it gave birth to. This was changed I think in remakes since Eggs were now present, but since Mewtwo was born in that universe and not "created", I question how there could be endless Ditto all over the Earth. (Recently in Black, I've been catching as many Ditto as I can in the Giant Chasm to get all the Natures. Mewtwo isn't related to the Giant Chasm.)
Mew is still the ancestor of all Pokemon, there were only 151 Pokemon discovered in the 1st gen then as more games came out they discovered more and more.
Remember though, the only reason new Pokemon are "discovered" are because Game Freak makes more games. Though Sinnoh was only introduced in Gen 4, it has always existed in that universe. And there have been a few in-game references to the existence of Pokemon beyond the games. (In Pokemon XD: Gale of Darkness, you encounter Bonsly and Munchlax before Gen 4 was released.)
But I realized something, since there is Pokemon like Kabuto, Aerodatyl, Omanyte, etc they could of lived before Arceus and Mew. If you ask me they're kind of like dinosaurs, so how do we know if they didn't live before them? Scientist have found fossils and believed them to be thousand's of years old.
Mew is said to have devolved into every common Pokemon, while Arceus is supposed to have been the first living creature to ever exist. For Mew, it is assumed to have became the fossils too, only they died out. For Arceus, they repeatedly hinted at it being the first Pokemon. I think the fossils were just unlucky Pokemon that died out for some reason.
Arceus didn't for say created the world it just shaped it. There's a big difference between creating and shaping something. So we still don't know who created the universe in Pokemon.
Something had to created Arceus after it created the world for Arceus to shape the world. After Arceus was created it created Palkia, Dialga, and Giratina to create dimensions.
Arceus's legend says it was born from an Egg that emerged out of a void of nothing but chaos. Then it is said to have created the world (possibly the universe). However, whether or not it created the world specifically to do it, or if something happened to Arceus after its birth that resulted in it sort of accidently creating the universe though is unknown. I feel that Arceus doesn't necessarily have to have played God and the universe's creation doesn't have to have been on purpose.
There's also another theory that could of happened with Mew. How do we not know mew was floating around the universe waiting. Mew could of been created with the creator of the world.
These are things that we don't know yet. Hell they both could of been created at the same exact time. Actually in the world of Pokemon what you call the "Big Bang Theory" could of happened and it created Arceus and Mew, we don't know. I'm not saying that it happened but it's definitely a possibility. But if Arceus doesn't need a universe to live then why should Mew?
The main problem I have with Mew being the first Pokemon is that there isn't anything in-game to suggest it. Arceus has several in-game references to its origin and an Event to show its creation powers. Mew has always just been there. The only in-game reference made to Mew at all is in the documents about Mewtwo. But even those documents can be pretty much simplified to "We found a Mew and cloned it, then the clone got mad and flew away."
And I'm not sure about suggesting there is a deity beyond Pokemon in that universe. We already have Pokemon that can control time, warp space, and represents antimatter. And since Arceus created those 3 Pokemon, I don't think creation of the universe is out of the question for a Pokemon.
Now lot's of Pokemon could for say be man made. I mean look at Porygon; it's said to have been hand made by humans. What about Mewtwo? He was created by Team Rocket so they can created the worlds strongest Pokemon to go on with they're plans.
Yes, there are plenty of man-made Pokemon. Porygon and its evolutions are always the first to come to mind. Then we have Castform for weather. And some poison Pokemon can be linked to human pollution, like Grimer and Trubbish. I'm sure there are others (is the Klink line said to be man-made?).
Other Pokemon like Onix, could of been created, it's very unlikely because rocks don't have a brain or move but in the world of Pokemon scientist can do different things. Scientist aren't like our scientist where they try to make the best electronical device they try to discover Pokemon and find out about the fossils and the legendary's, that's what I think.
But just because a Pokemon is Rock-type doesn't mean it is man-made. Just plain rocks may not have brains, but that doesn't mean a Rock Pokemon doesn't. I wouldn't consider a Pokemon to be man-made unless it is specifically said to be.