After much thought some the story and appearing pokemon have changed. The game will try to have as many pokemon from generations 1 to 5 as possible but the game will definitely have legionaries from all of those generations. the legionaries will play a massive part in the game more than usual in the main pokemon games. the story will now focus very much on arceus and the creation of the pokemon world but it will be different to the official pokemon games mythology. the game will also focus on a war between pokemon in which before recorded history the legendary pokemon or what the game will call 'Titans' fought each other after they were created to see which was stronger.
Also all titan pokemon can communicate with the player similar to the anime. in order to keep some link to the official pokemon games, mewtwo will not be classed as a 'Titan' as he was created by humans not arceus
as always please comment as your opinions are valued