What Is the Difference Between Clash of Ninja and Gekitou Ninja Taisen?
They are the same series wearing two names. In Japan, Tomy published Eighting's cel-shaded 3D fighters as Naruto: Gekito Ninja Taisen, literally Fierce Fighting Ninja Great War. When D3 Publisher and Tomy brought the series west from 2006, it was renamed Naruto: Clash of Ninja, keeping the numbering for as long as the two markets stayed in step: Clash of Ninja is Gekito Ninja Taisen 1 (Japan, April 11, 2003; North America, March 7, 2006) and Clash of Ninja 2 is Gekito Ninja Taisen 2 (Japan, December 2003; North America, September 2006).
Then the markets split. Japan received Gekito Ninja Taisen 3 in November 2004 and Gekito Ninja Taisen 4 in November 2005, completing the GameCube run; neither was localized. When the series moved to the Wii it split in two permanently: Japan got the Gekito Ninja Taisen EX line, four Shippuden games from December 2006, while the West got the Clash of Ninja Revolution trilogy, built on the same engine but assembled around the dubbed anime's slower progress.
So the honest answer to the difference is: none in origin, total in catalog. A Japanese GameCube shelf holds four games the West never officially saw, and the Wii shelves of the two regions hold different games that share technology and a name.
The full mapping
Full mapping: Gekito Ninja Taisen 1 and 2 equal Clash of Ninja 1 and 2. Gekito Ninja Taisen 3 and 4 are Japan only. On Wii, Gekito Ninja Taisen EX, EX 2, EX 3 and Special are Japan only; Clash of Ninja Revolution (2007), Revolution 2 (2008) and Revolution 3 (2009) are the international line, with Revolution built as an enhanced assembly drawing on Gekito Ninja Taisen 3 and the EX engine. The Revolution games were never released in Japan.
Names, boxes and region locks
The name change was cosmetic but the box art logic followed it: Japanese covers carry the Gekito Ninja Taisen branding under Tomy, Western covers the Clash of Ninja title under D3 and Tomy. Import copies are region-locked to Japanese GameCubes, which is why the Japanese discs historically traveled with Freeloader boot discs in Western collections, a pairing any honest listing of the Japanese games should mention.