Ah but once you get some volunteers- the adventurous sort, the Pokémon world is full of those- to prove it's good and safe, people will take a chance. The move will take some time, but will pay off once the majority of civilization is using the floating cities.
Or possibly 'man why are these young people dressing in such gaudy and impractical clothes?'
Kyogre also expands the seas using massive tidal waves. And besides, Groudon could just raise more land some amount feet a year. No harm done.
It certainly will take some time. It's going to take all the time for you to figure out how to transport enough goods and food all throughout the ocean to sustain as much life as there is right now.
And how is cosplaying as a pirate in the middle of Petalburg Woods practical?
But will they want to? So now you're going to be forcing people to do what they don't want to?