...what would you have? Basically all I have seen is the storylines to games being based of some bad guys who want to capture legendary/rare pokemon and use them for themselves...
I don't really remember the Gen 1 and 2 storylines, but based of team rocket.
R/S/E = Team Magma and Aqua, try and capture goudron or Kyogre and either make it rain or sunny so that land either drys up or becomes engulfed by sea.
D/P/P = Team Glactic, try and capture Palkia/Digala to control space/time
What I would like to see:
Maybe somewhere deep in the Gen V region, a rare/legend pokemon is sleeping, it wakes up occationally to walk around or feed. Then someone or something disturbes it so it cannot sleep and it goes into a rampage, destroying everything.
There is bad guys, with dark balls. One of them does manage to capture this creature and makes it evil (like how celebi was caught in dark ball) and the players goal is between becomming a top trainer, is to find the bad guys and have the legendary pokemon released so it can go back to sleep, and after it does, a while later you can go and catch it as it will want to battle you as you saved it.
In the mean time while your training and doing gym battles etc... some trainers pokemon get stolen and you have to rescue them from these bad guys and return them to trainers who give you exclusive items for their safe return.
Well, need more of a plot than that, but I don't know much right now and thats all I can think of.
What would you guys and gals want as a good plot?