JC was doing this stuff back before you could Google how to do it, or buy a book at your local B&N telling you how to do it. That counts for a lot. So does his consistent willingness to bring the fire down the mountain and hand it to the masses.
Additionally, post Quake 3, the team at Epic routinely chose better design tradeoffs for real world games. This includes both performance tradeoffs and spending of engineering effort on production needs (like a solid level editor). Hence the popularity of the Unreal 3 engine.