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A very popular design methodology in the software industry is the agile methodology. The agile method relies on fast iteration whereby you constantly present the client with new builds of the software and get feedback. Using ideas similar to the agile approach, game development can be made much more manageable. I found that my own personal opinions on this topic aligned with John Romero's when he was working on Doom, so check that out if you're interested in further reading.
Remove the concept of prototype
In your mind you should not …