I name my characters after the version. Red/Gold/Silver(Rival)/Crys(Girl)/Ruby/Saphire(I was upset that I couldn't spell Saphire properly; Girl), Dia, Pearl, Platina, Black, White, and since Black and White were used; I went with Hikari and Yami.
Not sure what I'll name X and Y characters, but I'll probably just start their names off with their titular character.
Official Gardevoir of the Pokemon X Message Boards
For White i named my FemC, Rika. Why? She gave me that vibe of Rika from Digimon Tamers. In white 2 I decided to rearrange the letters and end up with Kari. With X and Y I've got a few names going around but I think I am going to name the FemC, Lucy. The blond one. She reminds me of Lucy from Fairy Tail for some reason. So I guess it depends on the look of the character or, in Kari's case, continuity.
Summer of Juvia Lockser! http://i.imgur.com/Sg7Y6oU.gif http://i.imgur.com/VoQ8ekP.jpg http://i.imgur.com/P8XK3e0.jpg http://i.imgur.com/MnwAaWi.jpg