Why use Unity for Prototyping?
Unity is a great tool for rapid prototyping, it allows you to make changes quickly and build to a variety of different platforms without having to alter the code, which is handy too say the least.
We often build mobile games to HTML5/canvas which allows clients to play the game while development or changes are in progress without having to install APKs or Testflight. This allows a tighter team interaction and allows producers to see changes and work with them quickly.
We find even where the finished game will use a different engine or be coded natively to a platform (for example Unreal Engine or iOS or Android native builds) then Unity allows us to move much much faster with a prototype and that iteration allows a better final product once we move from prototyping and design into the productionisation/realisation phase of the game.
Unity is great for proof of concept work as you can quickly make a scene, shove in a few objects and get them doing what you want pretty quickly. It might not look great, but getting the mechanics down is fairly quick and easy.