I always pick a theme of nicknames for my main team, but most of the time the themes are like references to other video games I love. Like, I base some team on megaman, mother and zelda games.
For pokemon black, the nicknames were based on monsters/characters/etc of mother 3.
Eddy/Samurott - After Master Eddy!
Duster/Sawsbuck - Duster, mostly because it knew jump kick
Battyman/Swoobat - Mr. Batty or Battyman (his nickname because of his battle music)
Isaac/Bisharp - Isaac himself
Fuel/Reshiram - Fuel, I loved him & the name fits
Franklin/Gavantula - For the mighty Franklin Badge!