2 totally different games and this could possibly spark a fanboy war :s
They are both great games but I think overall, MGS4 takes the trophy. The attention to detail in every aspect is unbelievable. The cutscenes can get too much sometimes, but in the same way GoW i found to be linear and lacking in story.
It's just how the Oscar's work. A lot of great films and entertaining films are made every year, but it is mostly the artistic films that get the Oscar. MGS4 was artistic perfection to be enjoyed in several ways, whilst GoW was perfectly entertaining popcorn gaming.