KayJay has made a game mod for Natruo: Clash of Ninja Revolution 3. This patch changes the menu music, charakter menu music, and almost every stage. It also includes alternate outfits for Anko, Gaara, Shikamaru, Sakura, and Sasuke. Download the patch here, and hit ‘Read More’ for some videos.
ChaosDragon13 outlines what you need to do in this post. You need an FPK unpacker to edit the game’s FPK files, you can find one on the Tools page. You can find a discussion on changing the textures of Naruto: CONR3 here.
Game mod demo
Another video of the patch in action
Do u think u can change to characters complete model like baki into pein?
Yea. I don't have this game, but stuff like that's been done. You can swap in characters from other games from the same developer (8ing) too (like that Castlevania fighting game). Check out the Downloads/Media page for a few videos, or this forum thread for a veeery lengthy discussion on Naruto hacking. Throughout the thread ChaosDragon13 discovers how to mod characters in the game, then somewhere near the end they start talking about character swapping. I'd recommend starting from the latest post and working backwards.