Although it's kinda jarring in the case of the Sound 4, which were major antagonists in the Sasuke Retrieval Arc. And they were also given full movesets in the Ultimate Ninja series, also by Cyber Connect, so it's quite a base breaking topic among fans.
The Bus Came Back: Because this game begins roughly where the manga and anime begins, there are a number of characters who died or just fell into the background long ago but are featured here, most notably Zabuza and Haku due to popular demand. Some even get their own story mode chapters (see A Day in the Limelight below).
Colon Cancer: Although not present on the boxart, the title essentially manifests as this (Naruto Shippuden: Ultimate Ninja: Storm: Generations*
Arguably, a colon could also be considered for insertion between "Naruto" and "Shippuden"
). Just look at how many different fonts are utilized on the game's logo alone!*
Kage Summit Kankuro's Ultimate: "Secret Black Move: Flame Control Scorpion Show" may qualify too.
Combo Breaker: Just like with previous Naruto Storm titles, this one comes in two varieties. Substitution exists for precisely this purpose, allowing a character who's been hit to teleport somewhere else (but not necessarily somewhere safe). Support characters can also be deployed while the player character is getting attacked, forcing the attacking player to either dodge, put up a guard, or get hit by the support character.
Comeback Mechanic: When a character's HP is below a certain amount, his or her chakra gauge fully replenishes and he or she can enter Awakened Mode. In addition, a player's Substitution meter fills up while getting attacked but not while doing the attacking.
A Day in the Limelight: Each chapter of this game's story mode is centered around a different character or set of characters (except Naruto, who gets two). Some of these characters only appeared for a short while in the series, such as the chapter about Zabuza and Haku and the chapter about Minato.
Dream Match Game: There are plenty of playable characters in this game who have been killed off.
Early-Bird Cameo: Snake Cape Kabuto. Since this game doesn't cover the events of the manga introducing him, he doesn't feature in the story mode at all until The Stinger. And yet he's still made a fully playable character in Vs Mode. It's not until Storm 3 that he starts to figure in the story... in quite a significant role at that.
Nine Tails Chakra Naruto is this too. It's the Awakening of Five Kage Summit Naruto in this game, but in the Manga Naruto doesn't learn the ability until the arc directly after.
Easter Egg: Using Part 1 Hinata's Ultimate Jutsu on Part 1 Naruto results in a slightly different animation, as does using Karin's on Sasuke.
Fixed Floor Fighting: Most (but not all) of the stages are completely flat, though they're not necessarily the same size or shape. In the one stage that isn't completely flat (Uchiha Clan HQ), characters and projectiles go up and down the gentle stairs as if it was flat.
Joke Level: 'The Tale of Killer Bee', which consists of him rapping about his awesomeness and whoever he's fighting next. It really has to be seen to be believed. Gameplay-wise though, players will probably stop laughing once they face +100 Attack Kisame.
Lag Cancel: Combo-breaking is so easily done in this game that doing a full combo is impractical in most cases, so a new mechanic allows players to cancel a combo and make a hasty retreat.
Even Snake Kabuto is playable, despite not playing a role in the story until after this game is set. He doesn't even appear in the story mode until The Stinger. They really wanted everyone to be in this game.
The game does, however, omit some of the bonus costumes (Nap Mode Naruto and Hokage Naruto) as well as Lars Alexandersson.
Meet Your Early Installment Weirdness: The premise of this game. Young Naruto and Modern Naruto don't really meet besides in the introductory video, promotional artwork, and multiplayer modes, though.
Nerf: Previously, Sage Naruto, Minato, Deidara, and the puppet masters were able to trap players in high-damage moves that were difficult to escape from and could be re-initiated once finished. Not anymore—they have either been slowed down, or some mechanics now grant temporary immunity to these moves.
As far as non-character related nerfs go, Substitution has been changed from using bits of your chakra gauge to running on a separate meter altogether. Substitution was also assigned to a separate button from guarding, so there is no more of the "Substitution Dance" in previous games where people would just stand in one spot and press the guard button rapidly to negate any moves done to them.
No Kill Like Overkill: PTS Tenten's Ultimate Jutsu, Millin Blade Chaos. It was toned down from the Storm 1 version, but is still as over the top as ever.
Nonindicative Name: You don't actually get to play as Madara Uchiha in The Tale of Madara Uchiha. "The Tale of the Akatsuki" would have been a better title, but the developers probably couldn't fit all of the Akatsuki members' portraits on the "select story" screen.
Posthumous Narration: The narrator is Hiruzen Sarutobi, the Third Hokage, who died fairly early on in the series. He even speaks about his own death and funeral but continues to narrate the rest of the series' story anyway.
Power Creep, Power Seep: Many characters are just as good at fighting in this game as children as they are as teenagers or adults, if not better, despite the anime and manga itself showing them growing considerably stronger as they age. There are also some playable characters who are non-combatants in canon.
Spiteful A.I.: In Survival Mode, you fight up to 12 battles in a row, with minimal healing in between depending on how well you do in each battle. The easiest way to restore health is to get S Ranks. The easiest way to get an S Rank is to finish your opponent with an Ultimate Jutsu. On higher levels of Survival, the AI LOVES to spam "Balance" type Assist Characters (take an Ultimate Jutsu in your place) seemingly just to confound your attempts to do this.
Unstable Equilibrium: Survival Mode. As mentioned above, your health is only restored stightly between matches, depending on the time you took and your rank. But since one of the main factors in your rank is how much health you finished a match with, the more you get damaged the harder it is to get health back. This means that if you do badly early on, you'll have a really rough time later.
Walking Shirtless Scene: Kimimaro in battle - which is strange because his "versus screen" artwork shows him fully clothed.