1. Let players create quests through the NPC editor.
2. While it may be impossible for quest lines to naturally spawn due to random generation. The player should be able to create quest lines and narratives involving multiple NPCs and Boss trainers and Pokemon.
3. "Statue Quests" the ability to have statues give quests or battle in the form of stationed pokemon who don't despawn and can be added into quests.
4. Leveling NPCs. Similar to vanilla minecraft I beleive pixelmon NPCs should have a similar leveling system, where to gain a new level you have to complete a quest for said NPCs. I believe the community would happily help and quickly supply dozens upon dozens of unique NPCs with character based quests.
5. Commonality. Make basic quests more easy to obtain. Similar to mystery dungeon, I feel as if quest npcs or community boards with 3 quests should be available at Pokecenters.