I thought the *plot* in STALKER was great. I do know what particular story element you are referring to, and while it may not have been completely unexpected, the story about how you got there, coupled with how your actions determined one of several endings (at least 6 - and most of them "bad") when all was said and done I thought it was brilliantly done. And they did actually do a pretty good job of fixing the bugs (eventually) so that it became a great shooter in its own right. My biggest complaint with STALKER was the time spent trudging back to an outpost to sell or turn in quests.
COD4 was way too short, and after all the hype I was more or less disappointed in it.