There are plenty of tools for prototyping. I’ve always been a “Choose the right tool for the job” kind of guy. These are some examples of the types of prototypes I have built over the years.

Classic wireframes are the best IMHO for template-driven RWD. InVision means fewer flows and detailed annotations for simple interactions. Skittles Pawn Shop, Experience Design and Mobile Usability Testing Marvel is awesome for simple prototypes drawn on a whiteboard, for example Physical prototypes are a great idea when designing for an unconventional form factor. Flows intended for designers and developers to understand how a user goes through the desired experience. University of Toronto, Faculty of Medicine, HTML Prototype Mercedes-Benz Canada, Experience and Visual Design