As anyone who has seen a Pokeball in use can attest, scientists have perfected matter/energy conversion. With that kind of technology (and people such as Giovanni), it is nothing short of a miracle that the planet is still there.
Gyarados and Tyranitar... Their dex entries talk about maps needing to be redrawn if one of them should rampage, yet the overworld remains the same.
Anyone who touches (or was it hurts?) Azelf will lose the will to move in three days, which would seem to suggest that time moves differently in Sinnoh, enough so to stretch three days into an eternity.