To me it goes like this... MGS > MGS 2 >>> MGS 4 > MGS 3
I absolutely hated MGS 3 due to the storyline being set in the past and due to the camera HEAVILY HINDERING the gameplay (I played Snake Eater and didn't bother with Subsistence).
MGS 4 has great graphics and the storyline is all kinds of yumminess, apart from Naomi who I loved in MGS and is just a major bitch now. The game felt very light on gameplay though. As if I spent 1 hour watching a cutscene (which I don't mind when they're as well done as they were) and then I spent 10 minutes running and shooting, since stealth was basically not needed. It felt very meh.