Just to spice things up a bit, I like to maybe see a Tactics style game. I personaly really liked the system in Final Fantasy Tactics Advance. It'd be cool to have the trainer as anactive member in the battles. Maybe have different "fields" and objectives or different style battles. For example, battles against wild pokemon would be completely open and the wild pokemon could attack the trainer. Agaisnt other trainers the field would be a set size. But against baddies (Like Team Rocket) it'd be a kinda free for all Where the battle can also end of you knock out the opposing trainer.
As for a story line. I think we should keep the gyms and elite four since it part of the inrastructure of the pokemon world, but a quest which shifts the focus from them would be nice. There are ancient ruins scattered all over the official games, why not have that as the focus? The main character could be a young achiologist assistant who is part of a team of archeologist who discover a massive underground labrynth and your job is map the interior. From there, you could have Zelda style puzzles. And being that you play as an employee, the company your work for would have a varity of pokemon avalible; to keep people from hogging all the good ones, they would be issued on a timer system. That is, you have to return them after so many turns. Of course it'd be crap if you leveled something up like 10 levels and then lost it, so on your employee id card there'd be record of stuff like that. the more levels on your ID card the high level pokemon are avalible to you. As for the actual story, I don't really know. But there is ancient ruins and a Labyrnth, surely something interesting would happen. And something else that would be really cool. Instead of just a night and day system, why not have a days of the week system too. And since you are exploring as part of a company, why not get paychecks and time off, That is; after you work your required time you can go do stuff like sidequests or catch and train your own pokemon or even complete the gyms. I thought it was really cool in the Lost in Blue games where if you didn't sleep your character would begin to begin to fall over asleep.
Okay, I know it's beginning to sound like a sim, but I'm not suggesting all these things be placed in the same game (I would scream at a dungeon crawler with a tactics based battle system). Also, I realize that half of what I said above would be really hard or impossible, but I'm just throwing out ideas. Like the guys at the begining of this thread were saying, the old formula is stale and needs something fresh.
Even with all this creative juice, I really don't have a way to make it a reality, that is, aside from some Basic I used to write programs for te TI-83 and TI-84 calculators, I have no programing skills. I tried using Game Maker 7, but it bent me over it's knee and beat me like a 6 year old red headed step child.....that is, I'm a self proclaimed moron when comes to hacking. I did manage to install patches using IPSWin, but that is about it. (If you know that patcher, then you have realized the extend of my ROM hcking abilities. Sad, I know.) Anyway, that being said, if anyone would like to let me work with them and teach me towards creating something towards similar to what I layed out above I'd really appriciate it.