I have played pokemon since the day blue/red came out, and ever since those days back when I was 10 I have always dreamed of a game like this. When I was probably 10 or 11 when Pokemon Stadium came out. When I heard about it me and all my friends thought it was going to be a 3D game...I was very disapointed. I personally think it would be great for nintendo, they need something new on the block besides the same old Mario and Zelda (as great as they are) if they really wanna stick it to Sony and Microsoft. Just imagine....
You create your own trainer, clothes, color of skin, age, gender, all the good stuff in character creators. You get a Rival, you can create and name him or just take a random one. Then you start off in some town in Kanto, and instead of choosing one of the three normal starters, you pick any (non-legend, and not too powerull) pokemon out of the original 151+ the baby pokemon. Your rival also gets some random Pokemon. Over time you will meet a random boy and girl that will travel with you for the rest of your adventure, like your rival you can create them or get a random one. They will always have random pokemon though. Then instead of receiveing a lv. 5 pokemon, you get the egg, it goes to a cut scene of like "2 weeks later" and your in your room and the egg hatches as the pokemon you chose. You then have to do a few mini games to get your Pokemon's level up, because in show the diddn't only train by battleing, ash would have pikachu like iron tail a tree and that would get him stronger. Once you get your Pokemon to say level three through these mini games you set off on your journey. Like someone said earlier you do the gym badges in any order you please, the game will just recognise the next gym will be harder then the last. Pokemon are seen running around and you can either go up and battle them, or some will be aggrisive enough to attack you. Any Pokemon can be caught just about anywhere. Even pokemon that could not be caught in the wild in previous games like the 3 starters. Battling should not be turn based and like someone else said like super smash bros, were you have full controll over your pokemon and they can learn MORE THEN FOUR MOVES! Really how many moves does pikachu use...thunderbolt, thunder, agility, volt tackle, quick attack, Iron tail. Levelng will also be alot different, and harder. Say after you complete the Kanto region, your lucky if you have a pokemon over level 25. Evolutions will be alot different to. In the show pokemon dont evolve untill they do something really good, like acheive a major event, but it has to be past a certain level. Say after 7 gained levels under your controll, you get a specific mini game to do to evolve your Pokemon. The first time you do it it will be really difficult, but as your level gets higher it gets easier. Also every other level you go up you learn a new move, dodge, or jump. The moves will be yur standard say tackle, flamethrower, watergun, etc. Dodge will be like a upgrade system you start off with move out of the way, and your dodges get better over time. Jump will be either for pokemon who it is easy to jump with the height of there jump. Or for Pokemon who can use certain moves to aid there jump. Like say after a certain level bulbasaur learns how to jump with his vine whip.It will all hopefully make sence to you in the end. Once you win all 8 kanto bages, you go to the Pokemon league and do that tournament to see how you do.
Once you get the 8 Kanto badges and compete in the Pokemob leauge, you go to Johto. All the Pokemon will be higher levels in Johto, and the evolution thing will still work out with the mini games because you'll need to level them to get the mini games. You of course can put your regular party pokemon away and start new with johto pokemon, or use your current party to see how they do against the new regions pokemon.
This trend continues untill you collect all of the 32 available badges and thus beat the game. Once you get all the badges, new regions will be unlocked were you can go and try to catch all the ledgend pokemon. This makes it so this game stays true to the motto' "gotta catch em' all!" This game might be a little for one game disk to handle, so they might have to go final fantasy on us and make it a 3 disk thing. I would personally pay more then 50$ if a game like this came out.
Also every idea the "the beninator!!" thought of was great and should also be used in the game...If I said any of your ideas in mine sorry you can have all the credit.
I am really sorry for the length, I just kinda got going and never stopped