At franchise level I can say the MGS series is my favorite one. All three games from the original Solid trilogy are in my top ten games of all time, so I am by no means a hater of the series or of Kojima. He made those three games and for that he will always be a genius in my book. But ohh boy if I wasn't dissappointed by Guns of the Patriots. Worst MGS I've ever played. Actually it is the only one I haven't liked so far. I have yet to play Portable Ops, Rising and Ground Zeroes. Peace Walker was almost a return to top form story-wise until that ending with the robot-ghost singing and what they did to Paz happened, way to ruin such a lovely character just for the sake of shock and out-of-ass plot twists.
Back to MGS4. Snake deserved so much more. During the whole game Kojima shits on him. I've never seen a creator treat one of his most important characters so bad. I mean, dude gets old as fuck even though he is in his 40's (I know it's because he was genetically engineered that way, which sucks), his crush from MGS1 stops giving a damn about him as a woman and gets married with the guy who shits his pants. If looking old wasn't enough he gets a permanent big burn on half of his face, and when he finally finds out that his father is alive and it's Big Boss and starts sharing some father-son love he watches him die before his eyes because he gets killed by Snake's FOXDIE virus. And when everybody is partying in Meryl's wedding, even Otacon, his closest friend, he waits for his premature and inevitable death, alone... He deserved way better than that.
And that fucking moustache, I never liked it. If Kojima wanted the moustache so bad he should have left the beard as well. Some characters look good sporting a 'stache, Snake is not one of them. He looked better in the first posters of MGS4 when it seemed the game would take place closer to MGS2, when Raiden rescues Sunny from the Patriots:
In this artwork even gameplay mechanics are discussed. I don't know what happened during development but something tells me that MGS4 set in that time period would had been better and less batshit crazy (look at that badass Raiden):
The scene where Meryl and Johnny fight against all the FROGS, dear God... I remember the first time they are introduced to them in the game, Meryl, his whole team and Snake are there, and they are like "Holy shit (gasp)... guys, wait... it's the FROGS!! Liquid's personal guard!! If we joke around they will kill us all." In the cutscene where they are ambushed by just three FROGS, Snake and Johnny didn't even engage in combat because they didn't have nanomachines to communicate at lightning-fast precision with the rest of the team. That's right, they were so worried about confronting the FROGS that Meryl's fully-connected team minus Johnny took the lead. The outcome was each one taking one down, but one of the guys receiving a bullet. The fight lasted seconds, only three shots fired. There was no room for error. Fast-forward to the last part of the game and you have only Meryl and Johnny fighting against a shit ton of FROGS, coming nonstop at them, at the same time, and somehow they manage to beat all of them, while surrounded on a room's entrance, with Johnny without nanomachines, with both getting wounded, and while FLIRTING, declaring their love and shooting without even looking at them, Jesus Christ.......... At that point I seriously asked myself: am I playing an MGS game or am I watching some random generic romantic comedy?
Meryl's wedding, in general all of it but especially the part where she points her gun at Campbell's face, so overly dramatic, unnecessary and without reason, just to add artificial shock to the scene. And of course nobody gives a shit about Snake dying and being alone, it's all fun and laughs at the party. And speaking of over-dramatic I just remembered the part where Big Mama (horrible name, it sounds bad and I always think of Martin Lawrence in that fat suit) watches the body of Big Boss burning (which was actually Solidus'), and decides to walk over it for no reason, setting herself on fire, screaming and dying afterwards, instead of just trying to pull the body out of the fire,
Also when Raiden and Vamp are about to fight in Shadow Moses and a lot of Gekkos break in. The point of cutscenes is to feel like you are watching a movie, to be immersed in the story, that what you are watching is really happening in the universe of the game. Yet here they have Snake literally pulling a railgun out of his ass because hey that's how it happens during gameplay. Instead of thinking of a way to justify story-wise Snake carrying a railgun all the way through Shadow Moses or Raiden giving it to him to fight the Gekkos or whatever, they decide to be lazy and merge the cutscene with gameplay mechanics and having Snake pulling that stunt. Not satisfied with that it happened again minutes later, in the cutscene of Snake chasing Liquid at the port and the Mark II giving to him a long-ass assault rifle that obviously doesn't fit into its compartment but it took it out of there anyway because again that's how it happens during gameplay. It looks so ridiculous. And these weren't the typical in-gameplay little "cutscenes", these where full featured cutscenes with black bars at top and down, when you really get the feeling that this is happening in "real life".
Also REX getting back to functional form. That thing got tired of exploding once and again in MGS1, the flames were huge, the damn building was shacking from the inside out because of the explosions. Yet all that hardware damage, all that twisted metal, all those internal circuits destroyed can be fixed by Mark II with a software patch

I'm calling it, Otacon best programmer ever, not even Sunny can design software that fixes hardware. I really enjoyed the REX vs. RAY fight, it was so awesome, but goddamn that way of getting it back was so cheap, so forced, so fan service, as many other things in the game. The whole game felt like Kojima trying his hardest to emulate the bombastic style and cheese of a blockbuster Hollywood movie while forgetting what made the original trilogy so great: telling the story with his own style.
The part where they use the sort of catapults to board Liquid's submarine, God knows how many dozens of meters (if not over a hundred) they were thrown up in the air yet they land with no parachutes, no springs, no shock absorbers, no nothing, and not a single leg or arm was broken that day. Unbelievable. Again, lazy writing.
To say the plot was convoluted is an understatement. When you have to go to the extent of bringing the man himself Big Boss, who knows everything, back from his grave to painstakingly explain during like half an hour what's happening and still end up with the story as confusing as at the beginning of the game if not even more you know something is wrong. I mean, the game released its own official Wikipedia, for fucks sake. Someone could argue that we didn't put enough attention and that if you unravel the whole thing it makes sense, but I highly doubt it. Kojima himself has to resort to retcons every once in awhile to explain his own shit, and he already warned us of more retcons coming for GZ-TPP. So no, this is already past the point of not putting enough attention. MGS1 had the perfect balance between mystery and explanation, MGS2 just had those 10 minutes of crazy codec talk with Campbell toward the end but beyond that it was understandable, and MGS3 added more lore without confusing the player. But MGS4 just went full retard.
Ironically enough, this game made Raiden my favorite character. I didn't hate him in MGS2 but I didn't think he was cooler than Snake either. But MGS4 happened and Snake got shat, and Raiden was reborn. I think Raiden's story is the only good thing in the game. Something like that is what Snake deserved. Raiden got to kick ass, he looked cool, he was powerful, he was lethal, he saved Snake many times, he took care of Sunny, and at the end he even reunited with his own family, with Rose and his son! Yes, a son! Raiden is a father! How cool is that? Meanwhile Snake was treated like shit during the entire game, was owned like a bitch by Ocelot in hand-to-hand combat of all the things (the part where he uses CQC), was saved by Raiden, was saved by Meryl, was dumped by Meryl, was saved by Otacon, was saved by Drebin, hell he was even saved by Sunny (via software, and saved the entire world for that matter). He couldn't do shit on his own, and died alone like an old fart. This reminds me of the part in Skyfall where Q says to Bond that he could do way more damage from his computer in one hour than Bond could ever hope for in a year. The game felt just like that (except in the movie Bond gets a lot of shit done). No love or respect for Snake at all.
Bottom line, MGS4 was a fine game gameplay-wise, but a god awful MGS story-wise. I think MGS4 is to the MGS series what Alien 3 is to the Alien series, a decent movie on its own that when placed among the others shits on the potential of its predecessors.
MGS3 > MGS1 > MGS2 >>>>>>>>>>>>>>> MGSPW >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> MGS4
P.S. If you read through all this thank you for your time.