I agree with many points there, Groundon didant create the land it was an acient pokemon so he wasant around since the begining of time.
Bird trio- Many sets seen in Kanto atleast 5 sets and 1 set in XD and those eggs in snap.
Mewtwo- The hardest one to explain. They might of cloned more then one, like you said they must of cloned a Mew in r/b/y and a shiney Mew in fr/lg so atleast 2.
Mew- There was the one in Kanto which was extremely rare, and the one in Hoehn, which might be the shiney one, but the Mew in movie 1 is diffrent to the one in movie 7, it sounds different and loves to transform.
Dog trio- Again many sets, the most sets are in the Jhoto region, when one lots runs out of the burnt tower another lot might come in later, and Entei is also owned by a frontier brain.
Lugia/Ho- oh- Again this might be hard, theres more then 1 of each, the protector of Orre, and the many (atleast 3) around jhoto, like with the dogs when they move like get caught or run away beaten another may move in. There are also about 3 located in the sevil islands and a Lugia was probably stolen from Jhoto or Navel rock to create XD002.
Celebi- Its not clear yet, but there may be only a few left like Mew, we no theres atleast 2 so far, the one in the GS ball and the one in Orre at the shrine, and I agree in the movie I think that was the same Celebi aswell from different times.
Regi trio- I belive there are many of these sets residing in the same cave mabey 3 and battle revelution might have them in, also they are owned by a frontier brain.
Lati@s- There has to be loads of these, but most have died like in movie 5, there are mabey 2 of each left.
Groundon/Kyogre/Rayquaza- They are not creators of anything, just masters, like we are at pokemon. So there are a couple of sets only in Hoehn and they were caught by trainers and used in MT. battle. So theres about 2-3 of each I think still in Hoehn
Jirachi- Its realy Unknown about how many Jirachi there might be there might be only 1, more likely it might be more like the others and there has to be a shiney counterpart, but who knows?
Deoxys- We saw 2 in movie 6, so theres more the 1, I'm thinking about 3 or 4 of course it unknown about the space virus that causes them?
Psychic trio- I'm geussing theres more then 1 set, Emurrito seems to be the main one, mabey Nintendo are hinting the 3rd version might be based on it? There are mabey 3 of each. Just a hunch.
Diaruga/Parukia- Again its unknown about ow many there are there might be only 1 of each but probably 2 for their shiney counterpart.
Hiidoran- There a defenetly more then 1 of this badboy, becuase it can also be a bad girl and theres also the shiney boy/girl so theres mabey 3 of these non shiney.
Regigigas- Im geussing theres as many of these as there are sets of Regi, so mabey 4, 5 if you count the frontier leaders 6 for mt. battle trainers. But theres probably less mabey only 4.
Giradina- Theres not enough info, yet mabey theres more then 2 but I can't tell at the moment, probably 3?
Kureseria- It seems likekly also that there are many of these pokemon again i say 3-5.
Fione/Manaphy- There are loads of Fione as we can tell, but only 1 Manaphy? Or 2? The shiney?
Darkrai- It would be thinkable that theres more then 1, the shiney and there are many people who may see this pokemon in their sleep at once so there might be lots.
Sheimi- It seems to be a flower, thats about it, there are probably loads around shinou but trainers dont notice them because of its camaflage abilities.
Aruseus- Sounds like Seuz, anyway its the creation of all pokemon theres only 1, the shiney version might just be it transforming, or there might be 2.
So in conclusion, the Mewtwo of R/b/y was cloned of Mew but in fr/lg it might of been cloned of shiney mew, they might be set after and so they tryed to re-clone mew.
meaning theres atleast 2 of every Legendary, aruseus is still a mystery???