Kanto
>It is based on and named after the real Kantō region (関東, meaning "east of the barrier") in Japan.
Johto
Junichi Masuda has stated in his director's column that the kanji that inspired the name mean "castle palace" (城都) or "lattice-shaped palace" (条都)1; this meaning is connected to the city of Nara, which was the basis for Violet City.
Hoenn
>Junichi Masuda has stated that Hoenn's name comes from 「豊縁」 hōen, meaning "abundant relations", as a common theme in this region is the relationships forged between Pokémon and people.
Sinnoh
>Junichi Masuda has stated that Sinnoh's name is based on the term 神奥, which translates to "mysterious". The geography of the Sinnoh is based on the geography of the Japanese island of Hokkaido and southern part of the Russian island Sakhalin, as well as Kunashir, which is claimed by Japan, but administered by Russia. Sinnoh has been said to be an island like Hoenn, rather than a peninsula.
Unova
>Unova's Japanese name, イッシュ Isshu, is derived from 一種類 isshurui, meaning "one variety". According to the game director Masuda, this is to express that although the region is diverse in species and race, they are all the same as living creatures when seen from a distance.
The region's English name likely comes from the Latin words unum (one) and nova (new). It may also be derived from united, considering its basis on the largest city in the United States. It also sounds like parts of the phrase United States of America.
Kalos
>According to Junichi Masuda, the name "Kalos" comes from the Greek word κάλλος, meaning beauty.
As for how they pick a name, I suppose they'd pick terms/words/places based off of the theme of the region (eg. Kalos, having a appealing theme, comes from a word that means beauty)
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