Amen dude, I've been an MGS MANIAC since '02, and am just finishing up my 4th playthrough of MGS4 - I still feel it's the weakest story of the series, and I still don't quite get everything (SPOILER WARNING DING DING DING DING DING: if Ocelot/Naomi and Snake all actually wanted the same thing, to have that virus uploaded into GW and destroy the Patriots/Zero, why did Ocelot make Snake go through all that fucking hell to get to it, between all the FROG soldiers and the fucking microwave tunnel, rather than just holding Snake's hand and just taking him there himself?), but overall it's still a masterpiece, and Kojima is a true artist and brilliant man!
Honestly, though, I still think the original has by far the best story, writing, and performances! (and FUCK The Twin Snakes simply because they re-recorded all the dialog) Except for Liquid, he was kinda goofy