To be honest, this deserved to be pinned. I suppose I could give some more valid points in how to create the story since that seems to be the only front that has barely scratched the surface. Here's just a few points to consider when drafting up the plot:
1) Make sure that the player is involved in the story
Nothing is more boring than just have your character sitting there watching text wall after text wall with no say in it. Giving the yes and no option really helps. You can even go beyond that making alterations in the story and easy to miss dialogue that only occurs under certain conditions. It gives an incentive to explore and talk to more people instead of just trying to grind through the game as fast as possible. Story branches are rare, but I do not recommend huge ones unless the game is pretty short because it's rare for people to play a game more than once after it's beaten because it'd take to long to do the other branches.
2) Having knowledge in other areas of game making helps with the story planning
If you don't know anything about programming, it's kind of hard to create a story for a game. I've had to throw out ideas in the Revolution project solely because it'd be way too time consuming and a waste of time. Also with that programming knowledge, I'm able to have backup ideas just in case something doesn't work out. Field Effects too hard to make? I have a few alternatives to replace it. Even music knowledge can help as you can sync scenes directly to fit the song and timing.
3) Don't just throw a character in, incorporate them into the story
I'm going to be honest here: I'd rather play a game with 8 difficult gyms and a very strong, crisp story, than to have one with 18 gyms with most of the characters being nothing more than empty husks. The more characters you have, the more difficult it is to balance and implement them well. I know it's easy to make a plot with a lot of characters, but it's hard to do it well and give each leader a chance to shine and stand out.
4) Make sure you and your partners "equally" contribute to the plot
Some people are better at making a plot than others so it's never going to be equally be split equally. What I mean by it is that everyone should be contributing to it if they are working on the game. Obviously, the programmer should barge and be able to turn an idea down if it's not something they are willing to deal with and the director/leader should also have the power to turn something away if it's either against his vision or makes a huge plot hole. Make sure the group you choose to make an outline with is getting along otherwise, it'll either end up or mess or maybe someone vital might leave. I'll also add that the more people collabing on something mean more conflicts will arise as everyone will not agree on everything. 2-3 people is a very good number as it can cover one person's weaker areas with their strengths.
5) Be originally unoriginal
Let's be honest: it's next to impossible to make a completely unique and original plot. Use that to your advantage. People have certain expectations when it comes to a story and when something happens that they didn't expect, it'll catch their attention. I'll give you an example: almost all Pokemon games start with a professor giving out the starter. If you do something besides this, they're going to remember it as it's against the norm.
6) Realism is the key to a good story
Just because the story is fiction, doesn't mean everything has to. People are still people so they are still going to act in a certain fashion due to the situation. Half the reason Reborn is so good of a story is that it's based on real people and how they acted on the league. Often when crating any story, I try to think of how a character would react to a certain situation to get a better feel of their characters.
7) That Atmosphere is Important
Some of you may remember that old Pulse Tangrowth forest event that was scrapped for Episode 2's section. Why were so many people upset about it? It may have been nonsensical, but it had a fantastic atmosphere. Literally, you are walking through this forest alone, giving a feeling of dread...then you see Amaria and Florinia tied up by the vines. It gave a sense of fear for something bad coming. It was a well done build up for a pretty tense fight.
8) Don't create a dark story for the sake of it being a dark toned story
I'm not saying you can't make a dark story, but make sure there are lighter parts to it. If at every point in the story, you make something bad happen, you'll become a bit predictable. The simple, nice, and sweet points can make a bigger impact than even a surprise genocide if done well.
9) The story should be your best kept secret
The first time you read a story is completely different than any other times. For the Revolution project I'm working on, I often get criticized why I'm so secretive and don't share my ideas with the whole group. It's because I don't want to until they're finalized. Protect this thing at all costs especially the plot twists.
10) Limit you References
If you make a reference to some work or figurative person (let's say George W. Bush for example), not everybody is going to get the reference. I mean it's also fun to reference something (even GF does it once in a while), but splattering too many will just confuse people.