Namco Bandai Games Europe has posted a FAQ on their website officially confirming the Edo Kage, Kinkaku, Ginkaku, and the six missing Ninja Swordsmen of the Mist will not be playable in the game. They’ve stated it isn’t possible to include them through downloadable content (DLC).
There will be more DLC costumes in addition to the already released ones, but that’s it.
It’s always possible the next Naruto Storm game will have all the characters fans desire, but as for Naruto Storm 3, the chance is zero.
Naruto Shippuden: Ultimate Ninja Storm 3 is Namco Bandai Games and CyberConnect2’s fourth entry in the Storm series. It will be available for the Sony PlayStation 3 and Microsoft Xbox 360 in North America and South America on March 5, Europe and Australia on March 8, and Japan on April 18, 2013. The story for the game will begin with the Nine Tailed Fox incident from 16 years ago, continue on to the Five Kage Arc, and go up to the Shinobi War, covering the latest episodes of Naruto Shippuden as they air in Japan.