If that's the case, the plot with the sidequest should be related to the Pokemon having something to do with the plot at large, specifically something coming up, and the person going after it winds up being the only person able to follow it due to his/her skillset and/or background (IE, Craig being able to track an Absol through super-tall grass. and constant rain, or someone from Sinnoh allows him to understand two foregin grunts talk about a courier Skarmory delivering messages to their team): Victory in catching it means a leg-up for the rest of the team in the next major event.