I prefer MGS3 simply because of the way the maps were made and how the enemies were placed and how they react to different situations and the boss battles were awesome just the fact that you can complete the whole game without killing ANYONE is so awesome the hidden First Person Views are cool to find and the cutscenes overall.
Metal Gear Solid 2: Sons of Liberty became my favorite upon its release. The graphics were so alluring, the story was so intriguing, the sounds were incredible, and the gameplay of course was extremely dazzling. The first Metal Gear Solid was great too, but this one was definitely better. I liked the ones that followed, but not as much.
They were all great, but MGS3 stood out the most: story, gameplay and overall feel was just amazing. I never wanted to kill a villian as badly as I wanted the boss dead for betraying snake. But the ending made me rethink what the definition of a villian really is. Sometimes you don't get the whole story. MGS3 gave that other aspect and made me feel bad as a person, when I pulled the trigger on the boss. It didn't feel so good in the end.