As a long time MGS obsessor, I've been waiting for this game for 6 years (since the end of 2, cuz while 3 and PO were good, they hardly provided much resolution to 2's story), and I played the living hell out of it this past weekend, though am currently stuck at the fisticuffs battle with Liquid on top of Outer Haven. Honestly, my feelings on it are mixed so far; I haven't beaten it, so I can't totally make up my mind, but the things I loved are the unbelievable graphics, the REALLY fucking streamlined gameplay, the huge amount of exhaustively researched, realistic, customizable weapons, & the efforts to tie it all together. Also, the Beauty and Beast unit (especially Laughing Octopus and Screaming Mantis) were awesome boss fights and foxy as all hell.
However, even I, with all my love for the series, found some of the cinematics to go on a bit, though a big reason for that is probably that I started to get fishy on the plot after Naomi left and with the details of JD and GW etc. etc., so I found it hard to get too sad when Naomi died, for example, because it still seemed like she had betrayed them, but I don't really know how, and the S.O.P. system and how it relates to the nanomachines still kinda eludes me (did Naomi kill herself because she knew she was gonna destroy the SOP system, and thus deactivate the nanomachines which would kill her anyway?). I'll probably pick up the details on that after my multiple playthroughs, so that's not too much of an issue.
One thing that REALLY bugged me, though, was the handling of MGS3's characters - namely, that we're supposed to believe they all turned into a bunch of manipulative, twisted, power-hungry sadists? I mean, movie-loving, nerdy-but-cute Para-medic turning out to be Dr. Clark (mentioned in MGS 1), the one who tortured and experimented on Gray Fox before he killed her? And Major Zero being this architect of world conspiracies for murder, when in MGS3 he was this jovial British chap who loved James Bond movies, tea & crumpets, and describes Vodka as "sulfuric acid" - his codec calls were practically comic relief at times, so I really don't buy the fact that Kojima turned him into this evil mastermind of the Patriots. Same with Ocelot, and how he according to EVA he was a founding member of the Patriots, but in MGS2 constantly referred to them as a separate entity (I know they were an AI, but still) - honestly, I've always felt prequels were a bad idea, because it's seemingly impossible to realistically incorporate them into the story, and this reinforces that feeling.
Sorry if I got too in depth, but it is without a doubt my favorite VG series, and has been since 2001, so I was waiting a long time for this.