These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Crowning Music of Awesome: Final Valley Version 2 from Revolution 2 (originally from Gekitou Ninja Taisen 4), found only when Naruto faces Sasuke in a one on one battle in the Final Valley stage. And yes, it returns in Revolution 3, when the two face off again. Considering by that point you're a fairly experienced player, this can make the battle a Crowning Moment of Awesome as well if the match is between skilled players.
Also exclusive to said games, Crow. While he doesn't have many great combos, he doesn't flinch when attacked, so he can freely interrupt enemies' combos and even have some of them that involve carrying their target into the air, miss entirely.
Sasuke with the Sharingan has a strong attack (his upward one) which hits instantly and from across the map, with predictable results. He also has a regular combo which allows him to teleport behind his opponent and attack instantly, giving them no time to turn around and block. His normal version also had this move too, but it was a bit slower.
It gets a bit worse with his Shippuuden incarnation in Revolution 3, where he can teleport during a jump instantly behind the opponent anytime he wishes; this carries over to Gekitou Ninja Taisen Special. Expect this to be rather central to his gameplay, and nevermind that it cost a bit of chakra each use.
Kabuto regenerates most of any damage he takes, effectively giving him far more health than anyone in the game. His combos aren't bad, either. He also can reach VERY far with his neutral special attack, as his initial blow to start it (along with Tenten's) makes him lunge pretty damn far. It was fixed into a different initial blow since Revolution 3.
Itachi pre-Revolution 3 (in both Japanese and English version games) can spam his midair strong attack to rapidly drop clones on you for repeated pressure. He already has enough with his upward strong attack providing a similar effect as well (and that even leads into a combo).
From Shippuden EX 3, the stinger attack from Sasori's Hiruko form lets him break his opponent's guard in one shot from across the screen, his regular combos are almost as powerful, and his special attack poisons the opponent on top of its substantial damage.
Hand Seals allow characters to get a boost in attack and defense, which only happens if you are using a Wii Remote + Nunchuk controller.
A ton of characters from Shippuuden: Gekitou Ninja Taisen EX 3 had some broken Senzai Ninriki (Latent Ninja Powers) passives that had this in varying degrees:
Naruto's back strong attack which summoned his shadow clone no longer cost chakra, so most of the time opponents couldn't wait it out, or not even hit it either way to get rid of it (since they couldn't lock on to it like in a multiplayer battle). Temari could do this with one of her strong attacks that made her perform her summoning jutsu in the same vein as well.
Some characters, like Asuma and Sasuke (with Sharingan active) had one of their strong attacks unblockable while in said Ninriki State.
Kakashi is ironically a borderline case of the above, but is still game breaking; all of his moves took off a lot more on the opponent's guard gauge than usual, meaning he could guard crush as much as he wanted if he seized the momentum while in a pinch.
Yugao became a full on speed manic on all of her moves, making her hard to control but hard to pin down as well as making many of her basic combos very quick (though some could be easily messed up).
Kabuto, as if he wasn't bad enough, now recovers health with every attack he lands, giving him life steal.
Some characters' moves became doubled in their actions, like Shino's neutral strong attack and Kisame's Suikoudan no Jutsu down special (but causes 50% more chakra), and one of Sai's strong attacks made his artwork (the bird) fly back for a return strike after a set amount of time (which Kisame's case is much closer to). Deidara on the other hand could add 1 more clay spider bomb to his charged down strong. Guess what shenanigans it can lead to.
Hinata had her chakra Lag Cancels have no cost at all, making them free and she could have juggles and frame lock combos for days in the hands of a skilled player.
Neji and Gaara could automatically have their back strong and down strong attacks (respectively) active as a passive that always works against any projectile, so campers or characters with an actual need to zone their opponents have a lot less of a chance against them, arguably enough.
More of an annoying case than game breaking, hitting Hidan in his Ninriki state would make it so that you'd take a portion of the damage inflicted on him in return. Makes it a huge pain to even try to win against him with a perfect win round, as it was seemingly impossible. Though it could apply to some cases where against Hidan (like in a mission of some sort), you are to beat him without taking any damage, so welp....
It was bad enough that they reworked pretty much everyone's Latent Ninja Powers in Shippuuden: Revolution 3. Though some, like Kyuubi Naruto now having Super Armor, still stood up there. As well as others like true Sasori still being able to poison his opponent (but no longer reverses controls), Shikamaru's guard gauge never lowering, and some characters still keeping some of their old LNPs which may or may not be game breaking (but some like Sasori's and Asuma's were at least rebalanced however).
Growing the Beard: While Clash of Ninja/Gekitou Ninja Taisen 1 and 2 were decent fighters, they lacked depth in terms of value and combos. It wasn't until GNT 3(which never came out of Japan) rolled around that the series was being taken more seriously, adding more than one special for each character, aerial throws, and the best known combo cancel system. Gekitou Ninja Taisen 4 is the one considered best known and played by most fans, as it had fixed all the issues from the previous games, had 40 characters to play, built more upon the combo cancel system, and added new Three-Tag matches. However, that game did have quite a fewglitchesand bugs that were strange but at least fun....
However, a lot of depth and overall complete overhauls to the characters occurred in Shippuuden: Revolution 3, as a ton of new moves (like some new specials, new throws and redone strong attacks) and mechanics (new functions for some of their signature moves) for the characters have been added, as well as moves that only cost a small portion of chakra no matter what (unlike most that only drain chakra when held down/delayed). However, the game was also sadly, known for its poor online play via Wifi, especially since Revolution 2 had it completely removed.
Most if not all of these changes carried over for Japan in Shippuuden: Gekitou Ninja Taisen Special. Special also overhauled the tag-team system with a new bar solely for substitutions, separate from the main chakra bar; much like the recent and upcoming competitive Naruto games.
Hand seals have gained this. Introduced in GNT EX 2, players who used the Wii Remote/Nunchuk were given the chance to perform a certain motion control that can give a small burst of chakra, or boost defense/attack power. The problem? This mechanic is not available for Gamecube or Classic Controller players. TOMY's solution in Clash of Ninja Revolution 2 is the ability to turn it off for tournament players. However, in Revolution 3, if you play a match against the AI or an online match, they still can use it against you.
Of course, most of the mechanics that work only for the Wii Remote + Nunchuk combination tend to be this anyway, since none of the other controller schemes can make use of them.