Beat Batten is a client project, where we have been requested to prototype a game in 7 weeks that would expand the knowledge of the Batten disease to a wide target audience. Me and my team managed to deliver this as an online mobile multiplayer game.
More on Batten and the organization here: http://beatbatten.com/
I have created various iterations of prototypes within Unity. This proved to be very helpful for all members involved. It allowed the designers to test and iterate upon the game mechanics and dynamics. For the artists, it provided a reference for how the camera would be positioned and what the view of the game would be. Programmers could focus on networking the game instead of having to create the prototype.
Being a designer myself, there was very little stopping me from quickly testing and iterating new ideas, which was ideal for the game.
For level design (and later on also balancing) I created a custom tool where you could create, save and iterate a square tile-based level very quickly. This was great for rapidly testing and trying out designs without having to draw them manually or lay them out in an editor. Later on, I built a gameplay layer on top of it, where you could take turns and play a (visually) simplified version of the game.