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Sadly, Noppes/the Pixelmon Team have yet to release and API to incorporate lots of things into either mod. There are limitations to what you can do, such as:
-Custom NPC's cannot have Pixelmon.
-(that's all I can think of).
With that being said, I've always used the "Trader (I think)" from Custom NPC's to make Pixelmon shops. You know, Sell Pokemon drops for gold coins, and use the coins to buy Held Items, Poke Balls, and the like.