Like I've already said for that Super Nintendo Rob guy (I forgot his name already) in the past: "Anyone who thinks that Takamaru would be a Greninja clone is delusional."
I've tried my best to ignore this ignorance, but I'm afraid that I have to be Golden 2.0 in a silly scenario like this.
First of all, teleportation and becoming invisible ARE two different things. You disappear from sight in thin air and reappear else where, leaving behind a substitute in your original place. Invisibility makes you blend in with you surrounds and use that to your advantage in battle.
Shirukens aren't the only damn weapons he can wield in the first place. He has kunais, a Japanese throwing knife that he'd been using since his own game and it is WAY more iconic to him than shirukens in the first place. He also have Windmill Blades that are even more efficient that shirukens due to its boomerang like functionality. Then there's Nintendo Land's clay bombs which can easily be used to represent Ninja Castle way more than those irrelevant shirukens in the first place.
How the hell an anthropomorphic frog is considered similar to a Edo era human with obvious DIFFERENT proportions in the first place? Greninja is a Water/Dark type amphibian that wouldn't feel too out of place in Digimon and uses its own damn tongue for a scarf since it can't afford one. Takamaru is dress like anything you'd expect from ancient Japan with the ponytail to boot. The number of people who thing that they would be clones makes me want to murder a million Zubats.
There's a difference between wielding an organic katana and manipulation water for form weapons, people! He wields and fights like a true samurai with the stance and strikes to support that. Greninja is a athletic poor man's Dororo with the ability to use water in battle and we'd never seen him create weapons with it in Pokemon canon (Granted Sakurai had done so to make him a more efficient fighter like Lucario and Mewtwo). Takamaru would represent a samurai more than ninjas in the first place since he can't do martial arts and several samurai actually USED tools like shiruken or kunai to distract their foes from afar.
I think I've made my point just for all the Pokemaniacs to see.