what if its not a frozen world. You know how black and white have many differences, and one of the themes i got from them are the past and the future. So what if the world kyremu is in is either in the past or the future. so basically it be a area similar to like white forest or black city. And it could work by either choosing the light or dark stone to take with you. So it could work like this.
1. some point early in the game you get a choice of which stone to take dark, or light(which legendary you want)
2.you take one and N takes the other.
3.you dont find out N is the leader of team plasma untill way later in the game( thats why one of the stones are given to him)
4. A new character is acting like the head of team plasma( so N can do his thing)
5. Looker and the international police will play a part in the game.
6. At one point the new admin in team plasma will plan something that would put some pokemon in danger so you battle him and win but many plasma grunts comes for back up( your together with looker at this point) Then N will order them to stop thus revealing himself as the real leader of team plasma , saying stuff like he doesnt condone what the admin was doing so he allows looker to take him in.then it is revealed that N has one of the legendary pokemon and is planing to take over by becoming champion( since this will happen real late in the game it will be more emotional to find out N is your enemy since you would have seen much more of him thruout the game)
7. So you go the the city where the museum is and you talk like you do in BW but the gym leader revealed they recently dug out another stone but it was taken by team plasma. then it is reveal what the stones are and stuff.
8. so you do the eliet four like normal and fight N like in black and white.
9. after you beat him Ghetsis comes out and talks to you about the stone he has( the god stone) which will grant him the power to conquer the region by force. then the stone starts doing some crazy stuff and a rift opens up and ghetis goes thru it.
10. this is where the difference is if you have chose the light stone you go to a place in the past , if the dark you go to the same place in the future. you will get a whole bunch of back story from the people there ( it will be a area with a city and other stuff)
11. once you navigated thru you find ghetsis and he tells you about the place your in. you fight him with a new form of kyurem on his team.
12. once you win ghetsis is taken in and stuff and you return to the castle and N talks to you like in BW and the game ends.
13.Like before looker asks you to help find the sages but when you find them they will be with a plasma grunt and you will have a double battle with looker against the grunt and the sage.
14. After the all the sages are found N will contact you again with the news his father has escaped along with the plasma admin from before.
15. you go to a new area to find out ghetsis has open the rift again with a set of diferent stones you go back to the place and battle him again for good( at this point a whole lot of story comes out like Ns real name and stuff) and N takes them away
16. once you beat him you will notice the rift begins to expand which will place unova in danger so kyurem is there trying to keep it from doing it but it cant by itself
17. so your legendary comes outta its pokeball to help but it still not working. then you hear a voice which says something like blance can not be achieve with just light or dark but with both.
18. so one of the stone ghetsis had is left behind (the oppsite of yours ) start to react and opens a new rift , you go thru it going to the world you didnt go thru the first time ( the past, or the future) and are able to catch that pokemon( thus being able to catch both mascots in a single game)
19. once you return the the main rift the legendary you just caught will come and help the others closing the rifts expansion.
20. once every thing is over kyurem in his new form will come up to you, you will hear a voice( similar to when you meet darkrai) saying the pokemon wants to reunite with its long lost friends. so you deiced to take it. then the voice explains that kyurem was the reshairm and zekroms friend when they were one whole dragon, but when they broke apart they started fighting they opened the rift which would of destroyed unova so kyurem sealed it self within it to keep the homes of its best friend safe leaving behind the god stone. But before resharim and zekrom could help its friend they were sealed away by the people.
21. so after the story is finished the credits role but not before you see kyurem together with reshairm and zekroms as there original one pokemon together ( pretty much a mental picture kyurem sends you)
Now i know this will never happend but i think its a pretty good direction for the story to go you know