The Pokémon World is a dimension existing alongside the Reverse World.
Apparently, the Alpha Pokémon Arceus created the Pokémon World along with the Reverse World with Pokémon. Humans were also born through this and lived aside the Pokémon. Arceus also created the Lake trio Uxie, Mesprit and Azelf to represent knowledge, emotions and willpower. At some point, Mew came into being, carrying the DNA of all current Pokémon and creating the others, but going into hiding.
Arceus also created the Weather trio to represent the weather, Kyogre, Groudon and Rayquaza. However, people attempted to control Kyogre and Groundon with the Red and Blue Orbs, which lead them to become posessed and set Kyogre and Groudon fighting. Luckily, Rayquaza stopped the fighting and this seperated the Orbs from the people. The people then realized their mistake and sealed the orbs away.
Arceus then created the world using Regirock, Registeel and Regice to create Regigigas and it created landmarks around the area, with Mt. Coronet being the highest and left Heatran inside Stark Mountain. Once Regigigas' work was done, Arceus fell into a long sleep inside its own dimension.
Ho-Oh and Lugia also surfaced and lived seperatly in the Bell Tower and the Whirl Island. However, an earthquake broke the Whirl Island into the Whirl Islands and set a war in which the Bell Tower was burned and three Pokémon died. Ho-Oh then stopped the war and created Entei, Raikou and Suicune out of the ashes of the three Pokémon and all four left. A new Bell Tower was created, but Ho-Oh never returned. Ecruteak City was seemingly created to honour Ho-Oh for the deeds it did thousands of years ago.