pokemon has been getting lamer repeating the same basic story line (ash beats a gym or lose then do some massive training and wins by a hair) and Naruto is looking for Sasuke (Spoilier:He will never find Sasuke until Naruto Shippuuden which when he meets him he'll get beat up by him and he'll escape)
Pokemon games can crush Naruto games any day, but Naruto's plot runs circles around Pokemon's. I'd take Pokemon, because they have alot of sentimental value for me. I grew up with those games =).