It works either way. Ninjas can use the art of deception (Changing types with Protean) and Magicians can make stuff disappear (Taking items away with Magician).I feel you, this is the 2nd gen in a row where my favorite starter ends up being the weakest.....
It's even worse when I think that I've always felt like Greninja's and Delphox's abilities were swapped... I mean, isn't Greninja supposed to be all about the stealthy ninja rogue archetype? Why shouldn't he be the one with the ability to steal things? And don't magicians use their wands to transform stuff? Like, turning one element into another? Ergo what protean does?
Not really related to this specifically, but I don't really understand why people care about about what "tier" their starter is in (Especially if they don't play by that ruleset). Tier =/= how good the Pokemon is. There's obviously some crossover, but Pokemon can work above their respective tiers, and if they work fine where they, why do people act like they so desperately need to be changed? Not everything needs to be the best; my favourite Pokemon is NU and I can resist complaining about it.