I'd argue that they are kind of forced to.
The negativity towards the other 2 starters are really obvious, at least from Japan.
Well... Greninja was designed long before it was revealed (obviously), so at least its superior battling capabilities were a thing before the backlash happened. Then again, these battling abilities are because of a Hidden Ability, which does not affect in-game runs and therefore don't skew the balance in favour of it over the other starters.
I don't know at which point they could have decided to give Greninja by far the most exposure in the Anime, but episodes of animated series are usually produced well over six months ahead of their premiere. Maybe up to a year, or more. Anything Greninja does in the Anime today was probably decided on in the summer of 2015, if not before. When did Greninja start being overhyped in marketing and the TV series and such, compared to the two other starters? If it happened more or less one year after the release of the games, it could have happened because of the initial reception.
By the way, I'm also of the opinion that the tongue scarf makes Greninja stupid. It does not work well as a tongue. Actually, it would give Greninja both eating and breathing problems. It's unsanitary as heck. It serves no purpose as a prehensile appendage (and again, why did it have to be
its freaking tongue?), other than waving in the wind behind Greninja like a scarf (and tongues are generally
way too dense for that to be remotely realistic - it's a big muscle, not a gas-filled bladder). Last, as demonstrated by Jynx, Hitmonchan, Sawk, Throh, Farfetch'd and many others - Pokémon work
totally fine with using man-made or natural objects as part of their design. If they wanted to give Greninja a scarf -
why not give it a freaking scarf?!? Why did they have to make the scarf its tongue, or make its tongue a scarf? It makes no sense.
Hopefully, TPC will one day go out with a disclaimer saying that the scarf isn't actually its tongue after all. It is not referred to as such in Pokédex entries. It also seems like the creators of the Anime have problems with drawing it as if it was sticking out of Greninja's mouth, instead animating it like a conventional scarf. With scenes like
this in mind, I have hope that they will one day decide to call it a wholly separate body part. Because having a tongue wrapped around the neck like that is just plain idiotic.