As far i follow the pixelmon project, its difficult to find a pixelmon quest plugin, as you said, CustomNpc is good for that, but that requiere people to install another mods, for me, i make a sidemod that work with customnpc quest system and pixelmon, but its not for public server :/
Also, to give a solution for your problem i can suggest you theses sponge plugin :
- Quest plus plugin, by Justin
Monthly paiement 9.99USD
- MineQuest by Smackzter
I dont remember but maybe something similar
Hope it will help you !