predcon: Quake was in development, in one form or another, as soon as the original Commander Keen trilogy was finished. It's first incarnation was known as "The Fight For Justice", and in the game the player character was named Quake. A game usually gets a little weird when it goes through multiple rewrites and technology updates. Of course, once a franchise finds its direction, it becomes more defined. That's why Quake II was so much better.
I did not know that. Is there any pics of The Fight For Justice around?
I do know though, that the original ideas for Quake were much grander than the final product was. I remember one game magazine article from way back when, in which Sandy Peteres was hyping all those cool ideas, like injured enemis, which would try to run and hide, while leaving a blood trace you could follow and so on. There even was talk about RPG elements.