Oh... so sub-stories...
Hmmm...
There is always the option of cameos~ [with the old guy's digimon from Xros wars], these missions could give you a lot of EXP but you must defeate a boss / someone special.
Kuwagamon [Tai could give this quest], the digimon who chased everyone, who needs to be punished and reborn [Etc]
There could be a lot of missions like these by NPC-cameo.
Side quests umm...
Is there a back story to the NPCs? If there is, I could write something.