That is definitely true, but because Nintendo are the ones that publish the work that Game Freak does they could potentially have some say of what they might want into the games. Obviously they have to have some vision of their own for what they want to see, so it wouldn't be too far out of the realm of possibility for cameos in the form of clothing and accessories to appear!
Also as a totally different thing, I kind of hope we have the ability to customize our gear that's on our wrist some what. I mean, since it appears to be like a projector or maybe extendable like the Pokédex (unlikely, but who knows), so I feel like we'd be able to customize that as well. Stuff like its color, background, maybe even the ringtone that pops in for notifications like the Xtransceiver's tone.