There are many pokemon who shake the ground as a battle strategy, yet these earthquakes are extremely localized, to the point where an indoor pokemon gym, if built properly, can easily withstand even a powerful pokemon's earthquake. The major exception to this are the Whiscash, a pokemon once used in forecasting to predict large earthquakes at the expense of minor ones, but which were driven out of Kanto and Johto after leveling large metropolises in battle.
Before plate tectonics were fully understood, Whiscash were thought to be the source of all earthquakes, and the propensity of their large, curled whiskers to stand on end was believed to be a warning Whiscash shared with those they did not wish to injure. Today, it is understood that many (but not all) large earthquakes have nothing to do with the area pokemon, and in Hoenn they have become valued for their ability to predict earthquakes, even those they themselves cause – a habit those in other regions often deride as pure madness.
Whiscash can call Hoenn home because Team Magma does likewise. Team Magma does not expand the land by leveling hills and filling bays in the way land reclamation is done elsewhere, for this method offers little hope of conquering more than a tiny sliver of the sea. Instead, they use powerful ground pokemon such as Groudon to push out the land and raise the sea floor to rapidly expand the land's surface, a process which brings new earthquakes with every victory. Team Aqua do not use Whiscash to predict natural disasters, but to prevent disasters which are entirely man-made.