Here is some ideas for some minor side-quests that I think can add a nice variety to the Pokemon trilogy.

-(This is taken place in my idea of having a downtown area) As you walk by, you see a lady that seems concerned about something. You ask what is wrong and she tells you that her friend went missing and that she last saw her by a certain location (you choose). You go and investigate the area and you find her friend being harassed by a criminal. He keeps telling her to join him and his group of friends to go tour around a park (His backup story can vary). She keeps saying no and that she needs to find her friend to go to dinner (or something). You interrupt the man and he gets very annoyed. "Back off and mind your own business" he says and he starts challenging you to a Pokemon battle. You win and he backs down, the woman is happy and gives you her gratitude. You go back to the woman who was worried and she gives you a reward.

I will add more ideas in reply in the same post once I have thought about it more

Level Required: Moderate 10-20
Pokemon: 3 in hand (you can choose)
Reward: (your choice)
Exp: (your choice)

I saw some of your work for the project and I was wanting to help you out by giving some plot ideas for missions, story, character behavior, whatever. I will contribute in any way I can for this project as long as you can update me on your plans for the story.