When we want to make game, we have bunch of ideas in our mind for it. Like add different space ship in game, add different type of weapons, ammo, different enemies etc. If we add all those things then it become too many things, and every things becomes important. and when we try to implement all those things with additional things then it become quite complected.
At the time like this, making proto type of game is save lots of things. It will create base for your game. we can add many things once prototype of game is made.
It allows you to get quick feedback on your designs and it also helps you explore and experiment in a way working with more finished assets would prevent you from.
So, always make prototype of your idea first. It will provide you insight of what you can make, what you can add, and what you need for that.