Half Life 2 has a profound story in my opinion. Aliens take over earth easily, and withhold technology and rights unless you're willing to serve as their occupational police. Over time, humans sell their souls for quite human reasons, and become something other than human. Since a handful of people control the flow of information, this new thing that isn't quite human is presented as being the "evolution" of humanity - purging primate emotions and moving into a starfaring race. And best of all, there's no conversation where the bad guy sits you down for a heart to heart to talk about his ideologies - the ideas are all in the background of the game, and it's up to you to pick up on them and draw your own conclusions.
