- A non-linear, or at lest semi non-linear path. In that you are not always on one, straight path that railroads you to wherever you have to go next. And when you do get to a fork in the road, allow the player to choose a path, because I personally get seriously annoyed when I get to a point where there are many paths to take but one path is blocked by a guy whose text can be translated to:
"We don't want you to use this road yet, go on the other road and backtrack here. At that point the path will be open."
- More story-based game. More segments with evil team or whatever you are using to accompany the gym story. Have the gym leaders actually do stuff that matters. (Black and White sort of did this, but some leaders do nothing, and others do very small things.) In fact, have more characters in general do stuff that's important.
- Have the evil team not care about the local legend. Seriously, there must be more than one way to conquer the world. Having it so that the only way that the evil team can actually cause a threat is by obtaining unreasonable power doesn't make them look too tough, or competent. So, in general, if you are going to have an evil team, make them, you know, EVIL! Stop letting them be petty criminals that nobody really cares about.
- More competent evil teams. Do I even have to explain? I mean, how come a single child who just became a trainer take down entire evil teams but the local police, or the government, can't? Also, why does the evil instantly disband once a child beats their leader in a Pokemon battle? Does seeing their leader lose just make them lose the will to live?
And several other things I won't bother writing at the moment.