This could be fun. I mean, after all, the latest attempt of a DBZ CCG hijacked the Naruto game engine. Too bad that game wasn't more compatible - if the DBZ game had the same elements as Naruto, the two would meld together well, and we'd probably see a lot of people playing both.
My only real concern is the possibility of Ban Dai going overboard with this idea. Yeah, an initial set featuring lead roles from our favorite SJ manga (Ichigo, Luffy, Goku, and a handful of others come to mind) might be cool... But then fans might start clamoring for more, or one or the other company might see potential profitability in them, and we'd wind up inundated with non-Naruto characters invading the game.
That said, one of the things that keeps me hooked to this game is it's unique game engine - MtG may have invented the CCG, but I feel as though Naruto has perfected it, giving real depth of strategy to it in ways MtG has only begun to grasp. If Ban Dai produced games for other SJ manga that were fully compatible with Naruto, I would say let the crossover battle begin!