Maybe after you finished Poke-school then you would get a recommendation letter to go to other places to train!

That is an interesting feature especially for online games. It kinda gives everyone a role in battling and it makes people less cheap in the process. I'M IN FOR IT!

By adding different and fresh backgrounds, it makes the game seem more fresh and new. I was thinking it would be cool to make a Downtown in this game. Pokemon includes a lot of exploring (which is cool) but don't you think that an all-in-one would make things easier. For example you want to buy something hard to find and you do not know what specific location or area it is located in . The Downtown area could contain all of these specific items and with the danger of having some Pokemon Gangs suddenly attack you it could give more access to many side-quests as well! Add some jazzy music and some street lights along with many buildings and you may get yourselves a hit location .   

I wanted to make something truly original and new but i didn't want to ruin the overall feeling of the Pokemon trilogy and I do not know any plans for your current story so here is my plot from scratch:

You play as a  student that just transferred from another location and you have just reached the point of a big Pokemon test. You however, have absolutely no experience of battling so your teacher lends you one (Choose a starter Pokemon). You battle and pass your test as your teacher becomes impressed with your abilities. (Tutorial Ends) The teacher will have a large number of missions available depending on your grade level but you will soon encounter a new gang called "Team Ultimate" which plans on using illegal items and Pokemon to capture all of the Rare Legendary Pokemon in order to accomplish their goal. As you progress, "Team Ultimate" puts their goal into action by attempting on controlling and hypnotizing all the Pokemon in the world to do their bidding. In order to stop them, you need to be able to access new areas and grade levels by collecting Gym Badges. At one point you will see "Team Ultimate" scattered across different lands holding different Legendary Pokemon and you will need to capture 1 one them in order to throw the gang off balance. Since "Team Ultimate" has already captured the Pokemon, you will need to get hold of a illegal Poke-ball that captures the opponents Pokemon in order to temporarily foil their plan. There will be many other side quests also that will contain individual stories attached to them.

Features:

- Player Customization
- Team Battle
- Hm abilities
- Trade Menu
- Black Market (sell illegal items for lots of $$$)
- Downtown area (Includes Criminals, Black Market & Hidden gang base)
- Illegal Pokemon (Pokemon that have unbalanced abilities)
- Illegal Item (Disables a Pokemon from fighting a battle)(can only be used once and only on a person with multiple Pokemon)
- Multiplayer Tournaments
- Walking Pokemon that follow you
- A separate story (Play as a member of "Team Ultimate")

Like I said, since I do not know your original plans I made a new concept to the plot while still maintaining the Pokemon feel to it. 

I am only making a few pointers that applies to many and I mean MANY anime titles out there. (feel free to add)

All animes usually:

1. starts off with a character that does not know what is going on
2. has a character that knows almost everything
3. has a chick whether it be main character or random character that has abnormally large hooters
4. when says that the person is an average day high school student they NEVER are!

As i said before, these are only few to the many points out there and I will will not love anime any other way...