Kanto
Brock- as in Rock
Misty as in Mist
Lt. Surge as in Lieutenant, a military rank and electrical surge.
Erika- a species of flowers
Koga from Koga Ryu a school of ninjutsu
Janine - ninja with syllables reversed
Sabrina- sounds like Abra or Brain( or a reference to the teenage witch)
Blaine- as in Blaze or Flame
Giovanni- as in Geo
Johto
Falkner- as in a Falcon trainer
Bugsy- as in Bug
Whitney- as in white
Morty- From Latin, Mortis, Death or mortuary
Chuck- a reference to Chuck Norris
Janine-a jasmine is a sweet flower and the mine refers to mining
Pryce- as in Ice
Clair- rhymes with lair as in Dragon's lair
Hoenn
Roxanne- as in Rock
Brawly- refers to Brawl
Wattson- as in Electric Watts
Flannery- from Flame
Norman- as In Normal
Winona-from Winnow, wing or Wind
Tate and Liza- from Levitate
Wallace- from Water
Sinnoh
Roark- As in Rock
Gardenia- as in Gardening
Maylene- as in Melee
Crasher Wake- as in Crashing Waves
Fantina-a pun on phantom.
Byron- from Iron
Candice- Latin for Candida, which means shining white and as in ice
Volkner- as in Volt
Unova
Cilan - From Cilantro
Cress- from Watercress
Chili- from chili pepper
Lenora- Possibly from Normal
Burgh- from Bug
Elesa- from Electric
Clay- (obviously) from Clay
Skyla- (again obvious ) from Sky
Brycen- from Ice
Drayden-from dragon and den
More coming