The timeline won't ever fit. What I've come up with only fits about 100 years back, and according to pokemon anime history they've always been around (complete with ancient pokeballs etc). That said:
According to my history, the energy that pokemon have existed inside the earth and always has. In certain areas (i.e. volcanos, deep caverns, undersea vents like the Mariana Trench, etc) it could be released on a local level. Fossils have low-level exposure to it underground over millions of years, so while dinosaurs weren't ever pokemon, once fossil cloning becomes possible (as one of the emergent technologies) all the clones will develop as pokemon instead of their original species (this fits because to date, no one has cloned a dinosaur). A very few life-forms in a very few places (again, especially fault lines, deep caverns, and trenches) could be exposed and already have become pokemon in the present, so kyogre/groudon, mew, and a few others could already be in existence. Certain worship sites (like Stonehenge) could be based around natural energy upwellings, especially if they're near fault lines or are associated with the appearance of strange creatures. Az could have been associated with one of these (and maybe Stonehenge actually was a prototype Ultimate Weapon or something). Still probably not a full 3000 years old unless you bring Egypt into things, but I haven't worked anything out to that effect.
Some of the other time confusion, though not all, can be accounted for by a) people like the researchers actively sealing those parts of history away to prevent future nuclear war or Ultimate Weapons and b) superstitious beliefs, which probably become a lot more prevalent once mice become two feet tall and hurl lightning bolts - so several religions are formed around legendary pokemon and their existence is assumed to date back further than 100 years. That's the best I've been able to do; I know it will never fit entirely with established canon but it's not terrible.
One of the other "kinda cool" parts of my theory is that I figured out an explanation for evolution. All pokemon are born with energy, but it's not all in a stable state. The stable energy is what fuels their powers. The unstable part they can't use. As they mature, their energy levels increase. Eventually the unstable part hits critical mass (in some cases on its own, in others it has to be triggered by something) and the pokemon spontaneously decays into a more stable form. In this form, the total energy level is about the same, but more of it is available for the pokemon to use. Once all (or almost all) of a pokemon's energy has fallen into a stable state they won't evolve further, so the length of evolutionary lines is based on how stable that species' energy is to begin with. In general, legendary pokemon have entirely stable energy patterns, which means all of their considerable power is available to them and they only have one evolutionary form.
According to my history, the energy that pokemon have existed inside the earth and always has. In certain areas (i.e. volcanos, deep caverns, undersea vents like the Mariana Trench, etc) it could be released on a local level. Fossils have low-level exposure to it underground over millions of years, so while dinosaurs weren't ever pokemon, once fossil cloning becomes possible (as one of the emergent technologies) all the clones will develop as pokemon instead of their original species (this fits because to date, no one has cloned a dinosaur). A very few life-forms in a very few places (again, especially fault lines, deep caverns, and trenches) could be exposed and already have become pokemon in the present, so kyogre/groudon, mew, and a few others could already be in existence. Certain worship sites (like Stonehenge) could be based around natural energy upwellings, especially if they're near fault lines or are associated with the appearance of strange creatures. Az could have been associated with one of these (and maybe Stonehenge actually was a prototype Ultimate Weapon or something). Still probably not a full 3000 years old unless you bring Egypt into things, but I haven't worked anything out to that effect.
Some of the other time confusion, though not all, can be accounted for by a) people like the researchers actively sealing those parts of history away to prevent future nuclear war or Ultimate Weapons and b) superstitious beliefs, which probably become a lot more prevalent once mice become two feet tall and hurl lightning bolts - so several religions are formed around legendary pokemon and their existence is assumed to date back further than 100 years. That's the best I've been able to do; I know it will never fit entirely with established canon but it's not terrible.
One of the other "kinda cool" parts of my theory is that I figured out an explanation for evolution. All pokemon are born with energy, but it's not all in a stable state. The stable energy is what fuels their powers. The unstable part they can't use. As they mature, their energy levels increase. Eventually the unstable part hits critical mass (in some cases on its own, in others it has to be triggered by something) and the pokemon spontaneously decays into a more stable form. In this form, the total energy level is about the same, but more of it is available for the pokemon to use. Once all (or almost all) of a pokemon's energy has fallen into a stable state they won't evolve further, so the length of evolutionary lines is based on how stable that species' energy is to begin with. In general, legendary pokemon have entirely stable energy patterns, which means all of their considerable power is available to them and they only have one evolutionary form.
