I'm pretty sure they tried to plan every possible detail before starting production, because no one wants lose ends in a multi million dollar project. But the creative side of making games isn't a science. Something may look incredible fun on paper and later the players don't understand it or don't find a piece of fun. Or someone may come with a genius idea in later stages. In the end I think common sense dictates what to do. I doubt HL2 would be the same game without the gravity gun.
However I agree such decisions are quite risky and if you aren't Valve probably will derail most game companies ![]()