I'm sure it will ship with an Apple Remote. I also think Apple will have an app where you can control it from an iPod touch, iPhone or iPad.
A Remote App is fine when Daddy is home with the iPhone, but what are the kids to do while he is at work?
I'm thinking a Wii style remote in an Apple Remote form factor... with touch sensors... AND A WEBCAM for FaceTime... Yeah, That's the Ticket!!
Oh, wait. I forgot. It's supposed to have a $99 price point...
Ok, maybe the base unit will be $99 and there will be higher ends units... That sounds more like Apple!