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Pokemon don't spawn in the nether, so option 1;
Install worldedit and make a selection of the area you dont want pixelmon to spawn in, and run the command //setbiome hell
This will however change the colour of grass/leaves in the area so it's not always ideal.
Option two; on top of worldedit also install worldguard. define a region over the area you want to protect and give it a mob spawn deny flag, this will stop any mobs spawning in these areas and wont mess with the colour of grass/leaves etc. However you cant send your pokemon out in these areas either.