Question continues: “…would like to NOT face those. Some will maybe want to face certain Gym Leaders or Elite Four, while others would be afraid of them? I feel like this has the potential of being very annoying, but also it can be developed into a whole new game mechanic of managing Pokemon desires / convincing them of something. (For example, train a Pokemon against many Bug-types to make it less reluctant to face a Bug-type Gym Leader) What do you think?”
I very much think that this would be a good thing to have. I actually made a similar suggestion here and some other bits and pieces here, but in both cases it was sort of tangential to wider points I was making and I didn’t really talk about it from this angle. I sort of suspect that the reason Game Freak don’t try something like this is because of the sheer number of Pokémon that people often collect in the course of playing these games, and how utterly unmanageable it quickly becomes to try giving even a thin semblance of personality to each of them (that, and I can imagine it being very difficult to write this kind of content, given that Pokémon don’t talk). However, I think a kind of modular quest system along the lines you describe would have the potential to work quite smoothly – some quests that can be offered repeatedly by many Pokémon, others that can only happen once, some that are offered by Pokémon of a particular type, or species, or nature, maybe some that are triggered by things like using unusual items in battle or being knocked out under certain circumstances… and it doesn’t have to be all of your Pokémon doing this all the time in order to create at least a general impression that some of them, some of the time, might speak up with particular desires. Something similar worked for the Digimon World games, after all.
Pokémaniacal 