>>21913818Well, i believe that it was a design choice that came at a high risk but reaped high rewards. Think of it this way:
The Ninja motif had been done before with other pokemon. Using exo-physiological accessorizing on monster designs can be a dreaded shortcut when trying to convey a motif onto it, so in Greninja's case, i think the question was "How do we differentiate it from its previous evolutions while expanding upon its ninja motif?".
Shurikens, Masks to hide appearance and Scarves are nearly synonymous with ninjas, all of them were implemented onto Greninja's design, and i'm guessing when it came time to try to fit the scarf, the thought process went "How do we add the iconic scarf without it seeming like it appeared from nowhere?". The Why didn't i think of this before? result came after the realization that frogs have long tongues, so why not make it double as a scarf?
And there you go: A design that is coherent, believable and well executed. Hell, it's a prehensile scarf too, so that automatically makes it more useful than its worn counterpart, considering that he can use it to pummel or bind opponents, do escapes, etc.
It's not like he can't retract it whenever he needs to, you know? It's clever, awesome design. For all we know, he might still be able to use bubbles, we just haven't seen enough evidence in manga or anime to prove it.