Youre 13,youll probably forget about this when you grow up.
First,you want to make it 2d or 3d?
If its 2d,for PC,then its easier to make(but as a fan game).
For this youll need to know: programming,GIMP or Photoshop,you can use the midi files from VGMusic(giving credits to them),use the game sprites and textures from bulbapedia,cerebii.net), and thats about it.There are many free 2d engines out there you can use,with simple scripting.
But for 3d,its really different:making few hundred 3d models,texturing them,adding skeleton,animating,making the world,programming(3d engines-Ogre3d,Irrlicht,physics-ODE engine,PhysX,Havok engine,audio-OpenAL,FMOD engine),GIMP,Photoshop,etc for image processing.
Not to mention that the world would probably be huge-will run slow on older machines.
Thats the only way to make the game the way you want.Even if you become a great programmer and Nintendo hires you(not likely),youll still be doing what youre told.You wont be able to tell your word about creation of the world,if youll become a great 3d artist,youll do what youre told again,just make the world,but not the storyline.What im trying to say is you cant make it as you want as a Nintendo developer.
So,the only way you can make it is a Fan Project.