Naruto: Clash of Ninja/SCON4 vs CONR3
Gekitou Ninja Taisen! 4 (and by extension, Super Naruto: Clash of Ninja 4), as well as Naruto Shippuden: Clash of Ninja Revolution 3, are the two most played Clash of Ninja games in the community due to being among the last games of their respective console's series of GNT games (Nintendo GameCube and Wii, respectively), but despite being of the same game series, they play fundamentally differently. This page is intended to list the fundamental game differences between the two games, and give brief descriptions on how (or why) the two games are played differently.
Super / Gekitou Ninja Taisen! 4's Gameplay
GNT4/SCON4's gameplay can be considered a tight balance between long true combos due to the lenient combo gravity, and player expression through resets. The longer a combo goes on, the more meter the attacker gains, giving them generous amounts of chakra to threaten cancels and super finishers.
Damage from combos (and even to guard bars) is generally high. In addition, blockstrings require the defender to have advanced knowledge and precision on sidesteppable moves and points in strings, as sidestep invulnerability is short and front-loaded.
The substitution system was not perfected by this time however; substitutions have several blindspots thanks to cancels and positional manipulation (see Front Substitution). As a result, there are emergent techniques with a strong, OS-based combo game once substitution is available for the victim.
The gravity is consistently combo-friendly. However, everything scales this gravity.
Clash of Ninja Revolution 3's Gameplay
CONR3's gameplay places heavy focus on meter management, where optimal combos are necessary to have enough meter to defend yourself. The victim of a combo gains more Chakra than the attacker, and the longer the combo, the less meter you gain. The punish game is even more layered when putting the unique and universal "Paper Bomb" mechanic (L+R+A) into account; not only does this grant access to a projectile to nearly every character, it also allows players to reset combo gravity, both utilities for the cost of 1 bar (2 bars if you account for Y-Cancelling to throw one mid-combo).
Damage is lower in general because the amount of damage that can be dealt before giving the opponent the ability to sub is lower. Blockstrings are entirely mix-up based, as guard bars are much stronger than in the later GameCube games, and sidesteps have way more invincibility to compensate for the stronger tracking system. Well-delayed "stagger pressure" is a risky but important aspect to continuing a string on block when it's no longer safe.
The Substitution system has been buffed to where you can no longer exploit the position of it (front substitution removed). For certain moves (and even certain characters entirely, such as Sasuke and Yugao), Y-Cancels are way tighter to input. The attacker's meter gain is low, meaning you have to think hard when reading the opponent. Thanks to the "Ground Paper Bomb" (L+R+2A), another way of utilizing the aforementioned mechanic, you have a universal turn-around combo starter that lingers on the map for some time, allowing for you to use it as sub coverage in the future. You can also throw a Paper Bomb to similar effect in order to call-out substitutions.
Many characters are redesigned to have much more robust movesets; one of the most drastic examples is 
Hinata's Byakugan, which allows her to have some of 
Neji's moves and her base moveset at the same time (instead of Awakened Hinata being a separate character). The game also grants characters unique buffs when low on health called "Latent Ninja Powers" (LNP), which can change their threat level tremendously at that point: for example, 
Shino's LNP lets him always have the denser version of his 5A, and his bugs still drain chakra on block.
Combo gravity is physically heavier, compensating for the ability to reset it via Paper Bombs. However, non-physical moves (like kunai, elemental jutsu, swords, etc.) do not scale gravity.
Summary of Differences
- CONR3 gives combo victims much more chakra (and much faster) than GNT4/SCON4, making substitutions much more common. It can be considered an offensive maneuver to purposefully eat a hit to be able to substitute out of pressure and return to neutral.
- Gravity is noticeably stronger in CONR3 than it is in GNT4/SCON4. Landing supers after long juggles is considerably harder, if not impossible, from some combo routes.
- Back Throws are untechable in CONR3, meaning that off-axis Throws can be an even stronger mix-up and LKnJ > Throw is an easy and guaranteed damage punish.