It's just Nintendo's Style to have a common theme when naming certain things.
The theme of the Kanto Region is that most locations are named after a color such as Viridian City, Cerulean City and the Indigo Plateau.
The Theme in the Johto Region is that most locations are named from either a Flower, Plant or Tree such as Violet City, Blackthorn City and Cherrygrove City. Also note that planting berries was first made available in the Johto Region.
The theme of the Hoenn Region is that most locations consist of 2 words being put together such as Slateport City, Sootopolis City and Rustboro City. Hoenn may also be named after Flowers, Plants or Trees similar to Johto because of locations such as Lilycove City, Mossdeep City, Petalburgh City and Fortree City.
The Sinnoh Region doesn't actually have a theme. But it can be argued that it's theme is Space and Time.
The theme of the Unova Region could be based on "Clouds" since a few of the places seem to be named after types of clouds. (Nimbasa = Nimbus, Icirrus = Cirrus, for example.)
And lastly the theme of the Kalos Region is unknown at this point. It is based on France but I don't know whether or not that is it's actual theme. It's theme could be Life and Death based on Xerneas and Yveltal and AZ in the game but I rather doubt it.
As you can see from past Generations all of them except Sinnoh have a theme so you can see why all the Games are either named after a color, a gemstone and as of Gen 6 a letter.
If anyone feels they need to correct me at all in any of this feel free to comment and I'll edit my answer providing your comment is right of course :)
Hope I helped :)