I might do some when I have time, I was planning the bag, battle, etc systems and I came up with an idea, considering there will be shadow, normal and shiny pokemon and there will be tameness/happiness and pokemon have age and die at a certain point, depending on the way your pokemon are treated and how many shadow vs shiny you have there will be a Goodness Vs. Evilness bar to see if your a good or bad guy, if you have enough evilness you can go to a place where team smth (I still have to think about a name for it) gives you pokeballs that you can steal pokemon with, then after you win a battle you can pick 1 or 2 pokemon from the oponent and steal them, then you can either keep them or give them back to the base and get money for them. Being a bad guy you will also be able to convert any shiny/normal pokemon into a shadow/normal one.
If you are a good guy you can convert shadow/normal pokemon into shiny/normal and if you battle a bad guy (like a member of the team whatever) and win you can get 1 or 2 of their pokemon and take them with you, then you can keep them or give them for adoption at a pokecenter or sell them to the day care center :\
I might come up with some more ideas later, you can also give your opinion :P