The story mode. Some fans hate that the boss battles and free-roaming from Ultimate Ninja Storm 1 and 2 were removed, while others love the fully rendered cutscenes lifted straight from the anime and think that it's a fair trade off.
The lack of boss fights can be a Justified Trope on the fact that the team that made the boss fights for the previous game went on to be the main developer of the CyberConnect2-developed, Capcom-published game, Asura's Wrath, and both that game and this game were made and released in the same time frame within one another.
Good Bad Bugs: There's a glitch that lets you effectively set the handicap and AI level for Survival Mode. Given that the later Survival challenges are Nintendo Hard, this is very useful. See it in action here.
Hilarious in Hindsight: Now that Obito has been revealed to be Tobi, and the Masked Man can be placed on the same team as Tobi, you can make a three-man team consisting of the same person at different phases in his life.
On the High Tier end, pretty much every character listed under Nerf above. On the lower end, Killer Bee was bottom tier in the previous game simply because of the substitution mechanics really didn't favor him. He's a lot more useful now that they've been revamped.
Chakra Gun Volley also seems to have been rescued from being That One Attack due to slowing it down and increasing its charge-up time.
The final opponent in Killer Bee's story is Kisame...with +100 Attack. He can knock off 25% of your health bar (as much as a normal Ultimate Jutsu) with one Jutsu. No, not Ultimate Jutsu, regular Jutsu. If you let him get even a few hits or even a combo on you, it's pretty much over. Quite a shocking encounter in a chapter that's otherwise the epitome of Joke Level. One could say it's a LethalJoke Level?
Itachi. Doesn't help that he gets at least a 40+ power up whenever you fight him. His version of the Chakra Dash? Shapeshifts into a flock of ravens to attack you. What's worse it that any attack goes straight through the ravens, which makes sense because they're a product of genjutsu. Also, the AI is smart enough to know exactly what to do in most situations, in some, even better than you do! You also face him pretty early in the game, first time in "The Tale of Young Naruto Uzumaki." He also has Kisame to back him up there. Didn't practice before hand? Good luck...