When using Open Terrain Generator with pixelmon, pokemon do not automatically start spawning upon world load. You have to manually disable spawning through the config, then reenable. Only then will pokemon start spawning. Only tested on single player. Not sure if it's the same for server.

Pixelmon does not support OTG due to the way it registers biomes, so we are unable to help with this. If you want a biome changer mod, try Biomes O' Plenty, Real World, or Traverse!