Rapid prototyping is a key aspect of agile development, particularly with respect to games. In "The Art of Game Design," author Jesse Schell provides some excellent hints that will help you get the most out of your prototypes. I summarize his key ideas together with a few of my own below.
Before you begin, clearly articulate the questions you want to answer with your prototype. For example:
No prototype should try to answer too many questions. Prioritize your risks and focus on a single questions or a small set of closely related questions. Delay other questions for future prototypes or develop several prototypes in parallel.
Once you've decided on your questions, clarify how the prototype will answer them. For example, five users will play the prototype and answer the following questions (which you enumerate). Or, the prototype will test whether pygame can perform collision detection on 20 sprites (each 50x50 pixels) in full-screen mode at 30 fps.
The purpose of a prototype is to answer a question quickly. If you can't do it quick and dirty, your objectives are probably too broad.
This is related to the last one. Do not start thinking that you can "reuse" your prototype code. It is intended to be thrown away.
Your prototype doesn't have to be digital. Paper works better for many of the questions you'll want to ask.
Consider building your digital prototype with an easy-to-learn game engine like Game Maker or Pygame.